<PAGE>   1

     FILED WITH THE SECURITIES AND EXCHANGE COMMISSION ON NOVEMBER 15, 1999
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON D.C. 20549

                            ------------------------

                                   FORM 10-Q

     [X]   QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
        SECURITIES EXCHANGE ACT OF 1934

               FOR THE QUARTERLY PERIOD ENDED SEPTEMBER 30, 1999

                                       OR

     [ ]   TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
        SECURITIES EXCHANGE ACT OF 1934

         FOR THE TRANSITION PERIOD FROM ____________ TO ____________ .

                         COMMISSION FILE NUMBER 0-24457
                             BEYOND.COM CORPORATION
             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)

<TABLE>
<S>                             <C>                             <C>
           DELAWARE                          7375                         94-3212136
 (STATE OR OTHER JURISDICTION    (PRIMARY STANDARD INDUSTRIAL          (I.R.S. EMPLOYER
      OF INCORPORATION OR         CLASSIFICATION CODE NUMBER)       IDENTIFICATION NUMBER)
         ORGANIZATION)
</TABLE>

                            3200 PATRICK HENRY DRIVE
                         SANTA CLARA, CALIFORNIA 94054
                                 (408) 855-3000
              (ADDRESS, INCLUDING ZIP CODE, AND TELEPHONE NUMBER,
       INCLUDING AREA CODE, OF REGISTRANT'S PRINCIPAL EXECUTIVE OFFICES)

     Indicate by check mark whether the registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities and Exchange Act
of 1934 during the preceding 12 months (or for such shorter period that the
registrant was required to file such reports), and (2) has been subject to such
filing requirements for the past 90 days.

                              Yes  [X]     No  [ ]

     The number of shares of the registrant's Common Stock, $.001 par value per
share, outstanding as of October 31, 1999 was 36,249,622.  [ ]

--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
<PAGE>   2

                         PART I. FINANCIAL INFORMATION

ITEM 1. FINANCIAL STATEMENTS

                             BEYOND.COM CORPORATION

                     CONDENSED CONSOLIDATED BALANCE SHEETS
                                 (IN THOUSANDS)

                                     ASSETS

<TABLE>
<CAPTION>
                                                              SEPTEMBER 30,
                                                                  1999        DECEMBER 31,
                                                               (UNAUDITED)        1998
                                                              -------------   ------------
<S>                                                           <C>             <C>
Current assets:
  Cash, cash equivalents and short-term investments.........    $  86,959       $ 81,548
  Accounts receivable, net..................................       12,970          8,785
  Prepaid partnership agreements............................        6,914          4,091
  Prepaid expenses and other current assets.................       11,526          2,110
  Note receivable from a director...........................           --            270
  Cost of deferred revenue..................................       13,460          5,255
                                                                ---------       --------
Total current assets........................................      131,829        102,059
Non-current assets:
Property and equipment, net.................................        9,026          3,150
Deposits and other non-current assets.......................        6,674          4,695
Goodwill and other intangible assets, net...................      113,614             --
                                                                ---------       --------
Total Assets................................................    $ 261,143       $109,904
                                                                ---------       --------

                           LIABILITIES AND STOCKHOLDERS' EQUITY
Current liabilities:
  Accounts payable..........................................    $  12,356       $ 14,443
  Other accrued liabilities.................................       10,985          1,261
  Accrued interest expense..................................        1,528            483
  Current obligation under capital leases...................          118             --
  Deferred revenue..........................................       13,584          5,744
                                                                ---------       --------
Total current liabilities...................................       38,571         21,931
Non-current obligations under capital leases................           58             --
Convertible notes payable...................................       63,250         63,250
Stockholder's Equity:
  Common stock..............................................      295,262         69,311
  Deferred compensation.....................................       (3,087)        (2,226)
  Unrealized gain on investments............................          207             --
  Accumulated deficit.......................................     (133,118)       (42,362)
                                                                ---------       --------
Total stockholders' equity..................................      159,264         24,723
                                                                ---------       --------
Total Liabilities and Stockholders' Equity..................    $ 261,143       $109,904
                                                                =========       ========
</TABLE>

Note: The balance sheet at December 31, 1998 has been derived from the audited
      financial statements at that date.

           See notes to Condensed Consolidated Financial Statements.
                                        2
<PAGE>   3

                             BEYOND.COM CORPORATION

                     CONSOLIDATED STATEMENTS OF OPERATIONS
                    (IN THOUSANDS, EXCEPT PER SHARE AMOUNTS)
                                  (UNAUDITED)

<TABLE>
<CAPTION>
                                                    THREE MONTHS ENDED,             NINE MONTHS ENDED,
                                               -----------------------------   -----------------------------
                                               SEPTEMBER 30,   SEPTEMBER 30,   SEPTEMBER 30,   SEPTEMBER 30,
                                                   1999            1998            1999            1998
                                               -------------   -------------   -------------   -------------
<S>                                            <C>             <C>             <C>             <C>
Net revenues.................................    $ 36,599         $ 9,742        $ 82,020        $ 23,511
Cost of revenues.............................      32,285           8,281          70,809          19,943
                                                 --------         -------        --------        --------
Gross profit.................................       4,314           1,461          11,211           3,568
Operating expenses:
  Research and development...................       2,523           1,266           7,103           2,967
  Sales and marketing........................      24,178           7,928          61,359          14,026
  General and administrative.................       3,500           1,062           8,390           2,525
  Goodwill and deferred compensation
     amortization............................      12,069             487          25,105             980
                                                 --------         -------        --------        --------
Total operating expenses.....................      42,270          10,743         101,957          20,498
                                                 --------         -------        --------        --------
Loss from operations.........................     (37,956)         (9,282)        (90,746)        (16,930)
Other income (expense), net..................         174             384             (10)            241
                                                 --------         -------        --------        --------
NET LOSS.....................................    $(37,782)        $(8,898)       $(90,756)       $(16,689)
                                                 ========         =======        ========        ========
Accretion of premium on preferred stock......          --              --              --             (51)
                                                 --------         -------        --------        --------
NET LOSS APPLICABLE TO COMMON STOCKHOLDERS...    $(34,782)        $(8,898)       $(90,756)       $(16,740)
                                                 ========         =======        ========        ========
BASIC AND DILUTED NET LOSS PER SHARE.........    $  (1.05)        $ (0.33)       $  (2.73)       $  (1.04)
                                                 ========         =======        ========        ========
Weighted average shares outstanding used in
  computing basic and diluted net loss per
  share......................................      36,042          27,300          33,259          16,089
                                                 ========         =======        ========        ========
</TABLE>

           See notes to Condensed Consolidated Financial Statements.
                                        3
<PAGE>   4

                             BEYOND.COM CORPORATION

                CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS
                                 (IN THOUSANDS)
                                  (UNAUDITED)

<TABLE>
<CAPTION>
                                                                    NINE MONTHS ENDED
                                                              -----------------------------
                                                              SEPTEMBER 30,   SEPTEMBER 30,
                                                                  1999            1998
                                                              -------------   -------------
<S>                                                           <C>             <C>
OPERATING ACTIVITIES
Net loss....................................................    $(90,756)       $(16,689)
  Adjustments to reconcile net loss to net cash used in
     operating activities:
     Depreciation and amortization..........................       1,925             419
     Amortization of intangible assets and deferred
      compensation..........................................      25,105           1,090
  Changes in operating assets and liabilities:
     Accounts receivable....................................      (4,015)         (7,916)
     Prepaid expenses and other current assets..............     (12,405)         (7,781)
     Cost of deferred revenue...............................      (8,205)          1,328
     Accounts payable.......................................      (3,265)          4,467
     Other accrued liabilities..............................       1,894           2,797
     Deferred revenue.......................................       7,836          (1,578)
                                                                --------        --------
       Net cash used in operating activities................     (81,886)        (23,863)
INVESTING ACTIVITIES
  Purchases of short-term investments, net..................     (57,798)             --
  Costs associated with the acquisition of BuyDirect.com....      (5,849)             --
  Purchases of property and equipment.......................      (6,504)         (1,949)
                                                                --------        --------
       Net cash used in investing activities................     (70,151)         (1,949)
FINANCING ACTIVITIES
  Proceeds from issuance of notes payable...................          --           4,800
  Repayment of note payable to shareholder and director.....          --             (60)
  Repayment of capital leases...............................         (92)            (57)
  Proceeds from sale of redeemable convertible preferred
     stock..................................................          --           2,924
  Net proceeds from sale of common stock and exercise of
     stock options..........................................      99,150          48,833
  Capitalized costs related to common stock offering........         524              --
                                                                --------        --------
       Net cash provided by financing activities............      99,582          56,440
                                                                --------        --------
Net (decrease)/increase in cash and cash equivalents........     (52,455)         30,628
Cash and cash equivalents at beginning of period............      81,548           2,571
                                                                --------        --------
Cash and cash equivalents at end of period..................    $ 29,093        $ 33,199
                                                                ========        ========
SUPPLEMENTAL DISCLOSURE OF NON-CASH FINANCING ACTIVITIES
  Common stock issued in acquisition of BuyDirect.com.......    $120,542        $     --
</TABLE>

           See notes to Condensed Consolidated Financial Statements.
                                        4
<PAGE>   5

                             BEYOND.COM CORPORATION

              NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

NOTE 1 -- BASIS OF PRESENTATION

     The accompanying unaudited consolidated financial statements have been
prepared in accordance with generally accepted accounting principles for interim
financial information and with the instructions to Form 10-Q and Article 10 of
Regulation S-X. Accordingly, they do not include all of the information and
footnotes required by generally accepted accounting principles for complete
financial statements. The preparation of financial statements in conformity with
generally accepted accounting principles requires management to make estimates
and assumptions that affect the reported amounts of assets and liabilities and
the disclosure of contingent assets and liabilities at the date of the financial
statements as well as the reported amounts of revenues and expenses during the
reporting period. Actual results could differ from those estimates. In the
opinion of Management, all adjustments (consisting primarily of normal recurring
accruals) considered necessary for a fair presentation have been included.
Operating results for the three and nine-month periods ended September 30, 1999
are not necessarily indicative of the results that may be expected for the year
ending December 31, 1999. For further information, refer to the consolidated
financial statements and footnotes thereto included in the Company's annual
report on Form 10-K for the year ending December 31, 1998 filed with the
Securities and Exchange Commission.

NOTE 2 -- ACQUISITION OF BUYDIRECT.COM

     On March 30, 1999, a wholly owned subsidiary of Beyond.com merged with and
into BuyDirect.com, an online software retailer for consumers and business
customers. BuyDirect.com was originally launched as a service of CNET and became
a wholly owned subsidiary in March 1998.

     Upon the closing of this merger, Beyond.com issued 4,930,123 shares of its
common stock to BuyDirect.com's stockholders in exchange for their outstanding
shares of BuyDirect.com common and preferred stock. Beyond.com assumed options
to purchase 281,757 shares of its common stock in connection with the merger.
The common stock issued was valued at $120.5 million based on the average
closing price of the common stock for the five trading days immediately
preceding the announcement of the acquisition and the five trading days
following the announcement of the acquisition. We accounted for the merger using
the purchase method of accounting. The purchase price of approximately $139.1
million included the fair market value of the common stock of $120.5 million,
the fair value of the fully vested options assumed of $2.7 million, liabilities
assumed of $13.0 million and $2.9 million in acquisition costs incurred in
connection with the merger. The fair value of the unvested options assumed of
$4.6 million has been recorded as deferred compensation.

NOTE 3 -- SECONDARY PUBLIC OFFERING OF COMMON STOCK

     On April 14, 1999, Beyond.com completed the sale of 4,000,000 shares of its
common stock in a public offering, which generated net proceeds of $98.5 million
to the Company. Under the terms of this offering, selling shareholders
liquidated 1,000,000 shares of common stock. No proceeds from this portion of
the offering benefited Beyond.com.

NOTE 4 -- CONTRACT WITH INTELLISYS TECHNOLOGY CORPORATION TO SERVE INTERNAL
REVENUE SERVICE

     On June 16, 1999, Beyond.com signed a contract with Intellisys Technology
Corporation whereby Beyond.com will be the reseller of electronically delivered
and shrink wrapped software applications to the United States Internal Revenue
Service, will design and implement specialized online software stores, and will
implement proprietary electronic download managers targeting 130,000 IRS
employees and agents. The 65-month agreement is renewable on an annual basis.
Beyond.com recognized approximately $2.9 million of revenue related to this
contract in the nine months ended September 30, 1999.

                                        5
<PAGE>   6
                             BEYOND.COM CORPORATION

        NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (CONTINUED)

NOTE 5 -- ACQUISITION OF SOFTGALLERY SARL

     Beyond.com entered an agreement effective September 24, 1999 to acquire
SoftGallery SARL, a Paris, France based, leading European online software
reseller of digitally downloadable software products. Upon the closing of this
merger in October 1999, Beyond.com issued 247,000 shares of its common stock to
SoftGallery stockholders in exchange for their outstanding shares of SoftGallery
common and preferred stock; however, 80 percent of the Beyond.com shares issued
in the exchange, or 198,000 shares, are held in escrow and subject to
SoftGallery meeting specific European revenue targets and employment
contingencies. The shares held in escrow will be delivered in various intervals
over the next 48 months as SoftGallery meets the specific European revenue
targets and employment contingencies. The common stock to be issued is initially
valued at $3.2 million based on the average closing price of the common stock
for the five trading days immediately preceding the September 29, 1999
announcement of the acquisition and the five trading days following the
announcement of the acquisition. Beyond.com will adjust the value of the shares
to be issued related to the SoftGallery acquisition to reflect the current fair
market value of the common shares issued at the time the specific European
revenue targets and employment contingencies are met and the related shares are
earned. Beyond.com has not yet determined the total amount or allocation of the
purchase price. Beyond.com will account for the merger using the purchase method
of accounting. The purchase price will also include liabilities assumed of
$167,000, a cash payment of $500,000, and any acquisition costs incurred in
connection with the merger.

NOTE 6 -- LOSS PER SHARE

     Net loss per share is presented in accordance with the requirements of
Statement of Financial Accounting Standards No. 128, "Earnings per Share" (FAS
128). Pro forma net loss per share for 1998 has been computed under FAS 128 and
also gives effect to the conversion of redeemable convertible preferred stock
not included in net loss per share that converted upon completion of our initial
public offering. Pro forma net loss per share for the three and nine-month
periods ended September 30, 1998 were $0.33 and $0.72, respectively.

     If Beyond.com had reported net income, diluted earnings per share for the
three and nine months ended September 30, 1999 and 1998 would have included the
shares used in the computation of basic and diluted net loss per share as well
as additional common equivalent shares related to options to purchase 7,053,000
and 5,309,000 shares of common stock outstanding as of September 30, 1999 and
1998, respectively. In addition, diluted earnings per share for the three and
nine month periods ended September 30, 1999 would have included 3,449,000
additional common equivalent shares related to the convertible notes payable
(using the if-converted method).

NOTE 7 -- SEGMENT REPORTING

     During the year ended December 31, 1998 the Company adopted Statement of
Financial Accounting Standards No. 131, "Disclosures about Segments of an
Enterprise and Related Information" which establishes standards for reporting
information regarding operating segments in annual financial statements and
requires selected information for those segments to be presented in interim
financial statements. For all periods presented, we have viewed our operations
as principally one segment, software sales. As a result, all of the financial
information presented represents all financial information related to our
principal operating segment.

NOTE 8 -- RECENT ACCOUNTING PRONOUNCEMENT

     In June 1998, the Financial Accounting Standards Board issued SFAS No. 133,
"Accounting for Derivative Instruments and Hedging Activities," effective for
fiscal years commencing after June 15, 2000. SFAS No. 133 establishes accounting
and reporting standards for derivative instruments, including certain
                                        6
<PAGE>   7
                             BEYOND.COM CORPORATION

        NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (CONTINUED)

derivative instruments embedded in other contracts, and for hedging activities.
The Company currently does not make use of derivatives and management
anticipates that the adoption of SFAS No. 133 will not have a significant effect
on earning or the financial position of the Company.

NOTE 9 -- FOURTH QUARTER REFUND OF PREPAID ADVERTISING SERVICES

     In October 1999, Beyond.com decided to scale back its planned fourth
quarter television and radio advertising campaign. As a result of this decision,
Beyond.com was refunded approximately $8.9 million of prepaid advertising
services.

NOTE 10 -- COMPREHENSIVE INCOME

     Accumulated other comprehensive income presented in the accompanying
consolidated balance sheet consists of the accumulated net unrealized gains and
losses on available-for-sale marketable securities.

     The components of comprehensive income for the three and nine months ended
September 30, 1999 and September 30, 1998 are as follows (in thousands):

<TABLE>
<CAPTION>
                                              THREE MONTHS ENDED,                NINE MONTHS ENDED,
                                         ------------------------------    ------------------------------
                                         SEPTEMBER 30,    SEPTEMBER 30,    SEPTEMBER 30,    SEPTEMBER 30,
                                             1999             1998             1999             1998
                                         -------------    -------------    -------------    -------------
<S>                                      <C>              <C>              <C>              <C>
Net income.............................    $(37,782)         $(8,898)        $(90,756)        $(16,689)
Other comprehensive income
  Change in unrealized gain (loss) on
     available-for-sale investments....          68               --              207               --
                                           --------          -------         --------         --------
Comprehensive income...................    $(37,714)         $(8,898)        $(90,549)        $(16,689)
                                           ========          =======         ========         ========
</TABLE>

                                        7
<PAGE>   8

ITEM 2. MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS
OF OPERATIONS

     Certain statements in this Quarterly Report on Form 10-Q are forward
looking statements within the meaning of Section 21E of the Securities Exchange
Act of 1934, as amended, and Section 27A of the Securities Act of 1933, as
amended. When used in this report or elsewhere by management from time to time,
the words "believes," "anticipates," "intends," plans," estimates," and similar
expressions are forward looking statements. Such forward-looking statements
contained herein include statements relating to our intentions, expectations and
beliefs that we will continue advertising efforts to promote our brand,
arrangements with America Online, Excite@Home and Yahoo! will represent
significant distribution channels for our products, losses will continue at the
rate in which we are incurring in 1999, research and development expenses will
continue to increase in both absolute dollars and as a percentage of revenue, we
will continue to pursue branding, sales and marketing campaigns, that our cash
as of September 30, 1999 will be sufficient to meet our anticipated needs for
working capital and capital expenditures for at least the next 11 months, and
our systems, including components thereof provided by third-party vendors, will
be year 2000 compliant by the year 2000, and are based on current expectations
and entail various risks and uncertainties that could cause actual results to
differ materially from those expressed in such forward looking statements. Such
risks include the risk that actual benefits of arrangements with our strategic
partners will be inconsistent with anticipated benefits, that we cannot meet our
anticipated needs for working capital and capital expenditures as expected and
that we will not be able to access additional capital if required on terms
acceptable to us. For a more detailed discussion of these and other business
risks, see our annual report filed on Form 10-K pursuant to Section 13 or 15(d)
of the Securities Act of 1934 dated March 31, 1999, with the Commission.

OVERVIEW

     We are a leading online reseller of commercial off-the-shelf computer
software to the consumer, small business and large enterprise markets. Through
our online store (www.beyond.com), we offer customers a comprehensive selection
of software as well as related computer peripheral products, helpful customer
service, a convenient shopping experience and competitive prices. We believe
that our Beyond.com Web site is one of the most widely known and used sites on
the World Wide Web for the purchase of software. We deliver software to
customers one of two ways: either we physically deliver the shrink-wrap software
package or we deliver the software over the Internet through digital download.
We launched our Web site in November 1994 under the name CyberSource Corporation
and maintained a Web site named software.net. In December 1997, we spun-off our
e-commerce services business and changed our name to software.net Corporation.
In June 1998, we completed the initial public offering of our common stock. In
August 1998, we initiated an aggressive regional radio and national print
advertising campaign to promote the brand. In November 1998, we completed the
offering of $63.25 million aggregate principal amount of our 7 1/4% Convertible
Subordinated Notes. In December 1998, we initiated a regional television
advertising campaign and we changed our legal corporate name to Beyond.com
Corporation. We intend to continue advertising efforts to promote our brand in
1999 and into 2000.

     In March 1998, we expanded our third party sales channel by entering into
strategic relationships with America Online and Excite@Home, and in February
1999, we further expanded our third party sales channel by entering into a
relationship with Yahoo!. Under the America Online agreement, we are the
exclusive reseller of software on certain screens on the America Online service
and America Online's Web site, aol.com. On other America Online screens we are a
semi-exclusive reseller of software. Under the Excite@Home and Yahoo!
agreements, we have the right to display banner advertisements and links to our
Web site on certain Excite@Home and Yahoo! screens. In addition, Excite@Home
cannot display paid promotional links or banner advertisements of any other
software reseller on specified Excite@Home screens related to software.

     Under these agreements, America Online, Excite@Home and Yahoo! are
obligated to deliver minimum numbers of screen views with links to our Web site.
We call these screen views "Impressions." Under the America Online agreement, we
must make fixed payments originally totaling approximately $21 million. In
addition, under the Excite@Home and Yahoo! agreements, we must make certain
fixed payments to Excite@Home and Yahoo!, respectively, over the three-year and
18-month terms of the respective agreements. We also have agreed to pay America
Online and Excite@Home a percentage of certain transactional
                                        8
<PAGE>   9

revenues and, in the case of America Online, advertising revenues we earn in
excess of specified thresholds. In addition, we have agreed to make certain
performance-based payments to Yahoo! The America Online agreement terminates in
August 2001, the Excite@Home agreement terminates when Excite@Home has delivered
a certain number of impressions, but no earlier than April 2001 and the Yahoo!
agreement terminates 18 months after initial activation.

     We expect these arrangements with America Online, Excite@Home and Yahoo!,
to represent significant distribution channels for our products. If we, or the
other party to any of these agreements, elect to terminate any of the agreements
it likely would have a material adverse effect on our business. We cannot assure
that we will achieve sufficient online traffic or generate sufficient revenue to
justify our payment obligations to America Online, Excite@Home and Yahoo!, nor
can we assure that we will achieve sufficient online traffic or generate
sufficient revenue to satisfy our contractual obligations necessary to prevent
termination of the America Online, Excite@Home or Yahoo! agreements.

     Pursuant to our agreements with America Online, Excite@Home, Network
Associates, Yahoo!, Cnet, ZDNet, @Home, Roadrunner/Service Co. and Xoom we are
obligated to pay a total of approximately $35.4 million from September 30, 1999
through December 31, 2001, of which approximately $8.3 million must be paid
during the remainder of 1999.

     Over the past 18 months we entered into various agreements with Network
Associates concerning the online sale of software and the management of Network
Associates' Web sites. Network Associates is a developer of electronic commerce
locations and publisher of certain products marketed under the McAfee and other
names. Our agreements include a Co-Hosting Agreement and a Web Site Services
Agreement entered into in September 1998. Under these agreements, we agreed to
co-host Web sites with Network Associates and agreed to resell Network
Associates' products on Network Associates' Web site at www.mcafeestore.com. We
must make substantial payments to Network Associates for exclusive positioning
of links to our Web site on certain screens on Network Associates' Web sites,
and for rights to resell Network Associates products. If we or they terminate
one or all of these agreements, it would likely have a material adverse effect
on our business. We cannot guarantee that the volume of online traffic,
customers or revenues we obtain as a result of this relationship will justify
our significant fixed financial obligations to Network Associates.

     Each year since inception, we have incurred increasingly larger net losses.
These annual net losses increased from $1.5 million in 1996 to $5.4 million in
1997, $31.1 million in 1998 and $90.8 million in the nine months ended September
30, 1999. We anticipate our losses will continue at approximately the rate at
which we are incurring losses in 1999 as we expect to continue to incur costs
and expenses related to:

     - brand development, marketing, and promotion;

     - Web site content development;

     - strategic relationship development and maintenance;

     - technology and operating infrastructure development, including improved
       digital download capabilities;

     - increased headcount, facilities and infrastructure; and

     - assimilation of operations and personnel related to potential future
       mergers and acquisitions.

     In addition, as a result of the BuyDirect.com merger, we recorded a
significant amount of goodwill, the amortization of which will adversely affect
our earnings and profitability for the foreseeable future. We recorded goodwill
and other intangible assets of approximately $137 million, to be amortized
through 2002. We believe it is likely that we will not generate additional
earnings sufficient to recover the amount of goodwill and other intangible
assets recorded during the period in which they are amortized.

     Because we have relatively low gross margins, our ability to become
profitable given our planned expenses depends on our ability to generate and
sustain substantially higher net revenues. If we do achieve profitability, we
cannot be certain that we can sustain or increase profitability on a quarterly
or annual basis in the future.

                                        9
<PAGE>   10

     We base our current and future expense levels, which are largely fixed, on
our operating plans and estimates of future revenues. In view of the rapidly
evolving nature of our business, proposed and possible future acquisitions and
our limited operating history of selling software online, we have little
experience forecasting our revenues. Therefore, we believe that period-to-period
comparisons of our financial results are not necessarily meaningful and you
should not rely upon them as an indication of our future performance. If we
cannot achieve and sustain operating profitability or positive cash flows from
operations, we may be unable to meet our debt service obligations or working
capital requirements, which would adversely effect our business.

     We derive our revenues primarily from four sources:

     - sales of software to customers using credit cards, checks, and wire
       transfers;

     - sales of software to corporate customers that are invoiced directly under
       credit terms;

     - sales of software to various government agencies pursuant to contractual
       arrangements; and

     - to a lesser extent, amounts received from software publishers, hardware
       manufacturers, and other vendors for advertising and promotion.

     In addition, we also derive revenues from the sale of certain computer
peripherals, accessories, and internally developed applications. We recognize
our revenues from the sale of software, net of estimated returns, either upon
shipment of the physical product or delivery of the electronic product via
digital download. We defer net revenues associated with the sale of software
pursuant to contracts with the U.S. government that require us to provide
continuing service, support, and performance and recognize these revenues over
the period that we provide service, support, and performance. We recognize
revenues derived from software publishers for advertising and promotional
activities as the services are provided. Our U.S. government contracts are
subject to annual review and renewal by the applicable government agency.
Although all such contracts presently remain in full force and effect, the
applicable U.S. government agency may terminate such contracts without cause or
prior notice. Because the government contracts may be terminated without cause
or prior notice, we cannot be certain that we will generate any revenues from
U.S. government contracts in any future period. We recognize revenue from sales
of computer peripherals, internally developed software and accessories upon the
shipment of the physical product, at which time collectibility is probable and
we have no remaining obligations.

     On July 14, 1999, we launched the first in a chain of worldwide online
software stores in support of Symantec Corporation. These online stores will
offer Symantec's full range of software products to customers via digital
download or physical delivery. The initial online Symantec store was for United
States customers. On September 23, 1999 we opened additional Symantec stores to
serve customers in France, Germany, and the United Kingdom. In October 1999, we
opened additional Symantec stores in the Netherlands, Canada, and Italy. These
six international online stores are the first in a series of 11 planned
international online stores that Beyond.com will develop and manage for
Symantec. These international stores allow customers to purchase products in
local currencies and are written in the local language.

     In September of 1999, Beyond.com launched eStore, a service which offers
software publishers, hardware vendors and systems OEMs a full range of
e-commerce solutions including: website design and operation, marketing and
merchandizing support, transaction processing, physical and electronic
fulfillment, as well as customer services. eStore will allow Beyond.com's
business customers to sponsor their own professionally developed and managed
online stores by leveraging off of Beyond.com's proven online sales
infrastructure.

RESULTS OF OPERATIONS FOR THE THREE AND NINE MONTHS ENDED SEPTEMBER 30, 1999 AND
1998

     Net Revenues. Our net revenues increased from $9.7 million in the quarter
ended September 30, 1998 to $36.6 million in the quarter ended September 30,
1999. This increase primarily resulted from increased sales to consumer and
corporate customers and as a result of new U.S. government contracts.

                                       10
<PAGE>   11

     Our net revenues increased from $23.5 million in the nine-month period
ended September 30, 1998 to $82.0 million in the nine-month period ended
September 30, 1999. This increase primarily resulted from increased sales to
consumer, corporate and government customers.

     Cost of Revenues. Our cost of revenues consists primarily of the costs of
software and software licenses sold to consumer and corporate customers, related
credit card processing fees and the costs of software licenses and software
updates provided to the U.S. government. Our total cost of revenues increased
from $8.3 million in the quarter ended September 30, 1998 to $32.3 million in
the quarter ended September 30, 1999. This increase resulted from our increased
software sales.

     Cost of revenues increased from $19.9 million in the nine-month period
ended September 30, 1998 to $70.8 million in the nine-month period ended
September 30, 1999. This increase was primarily the result of increased software
sales.

     Gross Margin. Our gross margin (gross profit as a percentage of net
revenues) decreased from 15.0% in the quarter ended September 30, 1998 to 11.8%
in the quarter ended September 30, 1999. This decrease primarily resulted from a
higher percentage of revenue coming from lower margin government and consumer
customers. The margin on sales to consumer customers decreased as a result of
marketing rebate programs offered during the quarter ended September 30, 1999.

     Our gross margin deceased from 15.2% in the nine month period ended
September 30, 1998 to 13.7% in the nine month period ended September 30, 1999
primarily as a result of a higher percentage of revenue coming from lower margin
government and corporate consumers, offset slightly by a $600,000 sale of
internally developed software to CyberSource which had no corresponding costs in
the 1999 period. In the future, we may expand or increase the discounts we offer
to customers or otherwise alter our pricing structures and policies. If we take
such an action, it may have an adverse impact on gross margin in future periods.
Further, although we strive to increase the percentage of traditionally higher
margin consumer business, higher margin digital download revenues, higher margin
sales of internally developed software applications and higher margin
advertising and promotional revenues as a percentage of our total net revenues
in future periods, there is no guarantee that we will be able to do so. In
future periods our gross margin may decline if the revenues we generate from
sales to the U.S. government or sales to large enterprise customers continue to
increase as a percentage of our total net revenues.

     Research and Development Expenses. Our research and development expenses
primarily consist of personnel and other expenses associated with developing and
enhancing our Web sites as well as associated facilities related expenses. Our
research and development expenses increased from $1.3 million in the quarter
ended September 30, 1998 to $2.5 million in the quarter ended September 30,
1999. These expenses decreased as a percentage of net revenues from 13.0% in the
quarter ended September 30, 1998 to 6.9% in the quarter ended September 30,
1999. This increase in absolute dollars primarily was the result of increases in
our personnel and depreciation on computer equipment.

     Our research and development expenses increased from $3.0 million, or 12.6%
of net revenues, in the nine months ended September 30, 1998 to $7.1 million, or
8.7% of net revenues, in the nine months ended September 30, 1999. This increase
in absolute dollars primarily was the result of increases in our personnel and
depreciation on computer equipment. We anticipate that our research and
development expenses will continue to increase in absolute dollars in future
periods.

     Sales and Marketing Expenses. Our sales and marketing expenses consist
primarily of promotional expenditures and costs associated with operating our
Web sites, including personnel and related expenses. In addition, we include the
expenditures associated with our strategic marketing alliances under sales and
marketing expenses. Our sales and marketing expenses increased significantly
from $7.9 million in the quarter ended September 30, 1998 to $24.2 million in
the quarter ended September 30, 1999. However, as a percentage of revenues,
these expenses decreased from 81.4% in the quarter ended September 30, 1998 to

                                       11
<PAGE>   12

66.1% in the quarter ended September 30, 1999. This absolute dollar increase was
primarily the result of costs associated with:

     - developing and maintaining our strategic marketing alliances;

     - a branding and marketing campaign (including expenses associated with our
       re-branding efforts); and

     - an increase in personnel to support increased sales and marketing and
       advertising expenditures.

     Our sales and marketing expenses increased from $14.0 million, or 59.7% of
net revenues, in the nine months ended September 30, 1998, to $61.4 million, or
74.8% of net revenues, in the nine months ended September 30, 1999. This
increase both in absolute dollars and as a percentage of net revenues was
primarily the result of costs associated with developing and maintaining our web
site, our branding and marketing campaign, and an increase in personnel to
support increased sales.

     We intend to continue to pursue branding, sales and marketing campaigns. In
addition, our current strategic marketing alliances with America Online,
Excite@Home and Netscape and Yahoo, in addition to the alliances with Cnet,
ZDNet, @Home, Roadrunner/Service Co. and Xoom in the BuyDirect.com merger,
require us to make payments totaling approximately $52.5 million over the terms
of those agreements. As of September 30, 1999, approximately $35.4 million of
this amount remained to be paid. We are expensing the costs associated with the
America Online and Netscape agreements ratably over the terms of the respective
agreements. We are expensing the costs associated with the Excite@Home agreement
as costs are incurred and payments become due. We are expensing the minimum
payment amounts over the three-year term of the Co-Hosting Agreement with
Network Associates. We may enter into similar strategic marketing alliances
requiring significant minimum payments in the future and, as a result, we may
substantially increase our sales and marketing expenditures. Due to our
branding, sales, and marketing efforts and our financial commitments associated
with our strategic marketing alliances, we expect sales and marketing expenses
to continue increasing in absolute dollars in future periods.

     General and Administrative Expenses. Our general and administrative
expenses primarily consist of personnel expenses, legal and accounting expenses,
and corporate facility-related expenses. Our general and administrative expenses
increased from $1.1 million in the quarter ended September 30, 1998 to $3.5
million in the quarter ended September 30, 1999. These expenses decreased, as a
percentage of net revenues, from 10.9% in the quarter ended September 30, 1998
to 9.6% in the quarter ended September 30, 1999. This decrease as a percentage
of net revenues was primarily the result of a relatively slower rate of hiring
in the executive, finance, and human resources functions. However, general and
administrative expenses increased in absolute dollars as a result of increased
personnel-related costs and facilities-related expenses.

     Our general and administrative expenses increased from $2.5 million, or
10.7% of net revenues, in the nine months ended September 30, 1998, to $8.4
million, or 10.2% of revenues, for the nine months ended September 30, 1999.
This decrease as a percentage of net revenues was primarily the result of a
relatively slower rate of hiring in the executive, finance, and human resources
functions. However, general and administrative expenses increased in absolute
dollars as a result of increased personnel-related costs and facilities-related
expenses. We anticipate that these expenses will continue to grow in absolute
dollars as we incur additional expenses associated with transitioning from a
single site operation to multiple and international site operations.

     Amortization of Deferred Compensation and Other Intangible Assets. Expenses
associated with the amortization of deferred compensation and other intangible
assets related to the acquisition of BuyDirect.com in March 1999 and the grant
of stock options, increased from $487,000 in the quarter ended September 30,
1998, to $12.1 million in the quarter ended September 30, 1999.

     Expenses associated with the amortization of deferred compensation and
other intangible assets, increased from $980,000 in the nine months ended
September 30, 1998, to $25.1 million in the nine months ended September 30,
1999. This increase was primarily the result of the amortization of intangible
assets related to the acquisition of BuyDirect.com. We expect the amortization
of goodwill and other intangible assets to remain at these levels in future
periods. Additionally, we believe it is unlikely that we will generate

                                       12
<PAGE>   13

additional earnings sufficient to recover the amount of goodwill and other
intangible assets recorded during the period in which they are amortized.

     Interest Income and Expense, net. Interest income, net, consists of
earnings on our cash investments, net of interest costs related to our financing
obligations. Interest income, net, decreased from $384,000 in the quarter ended
September 30, 1998 to $174,000 in the quarter ended September 30, 1999. This
decrease was primarily a result of interest expense related to the 7 1/4%
Convertible Subordinated Notes offset by higher average cash balances related to
proceeds from our secondary offering.

     Interest income and expense, net, decreased from interest income of
$241,000 in the nine months ended September 30, 1998 to interest expense of
$10,000 in the nine months ended September 30, 1999. This decrease was primarily
a result of interest expense related to the 7 1/4% Convertible Subordinated
Notes partially offset by higher average cash balances related to proceeds from
our secondary offering.

     Income Taxes. No provision for income taxes has been recorded due to
operating losses with no current tax benefit.

     As of December 31, 1998, the Company had federal and state net operating
loss carryforwards of approximately $37,000,000 and $31,000,000, respectively.
The Company also had federal and state research credit carryforwards of
approximately $314,000 and $268,000, respectively. The net operating losses and
credit carryforwards will expire at various dates beginning in 2002 through
2018, if not utilized. The net operating loss carryforwards differ from the
accumulated deficit primarily as a result of the accounting for the Spin-off of
CyberSource to the Company's preferred and common stockholders on December 31,
1997.

     Utilization of the net operating losses and credits may be subject to a
substantial annual limitation due to the ownership change limitations provided
by the Internal Revenue Code of 1986, as amended, and similar state provisions.
The annual limitation may result in the expiration of net operating losses and
credits before utilization.

LIQUIDITY AND CAPITAL RESOURCES

     From inception through September 30, 1999, we financed our operations
primarily through private sales of preferred stock, proceeds from our initial
public offering of 5,750,000 shares of our common stock, sales of our 7 1/4%
Convertible Subordinated Notes, and proceeds from our secondary public offering
of 4,000,000 shares of our common stock. We raised cumulative net cash proceeds
totaling $14.8 million through private sales of preferred stock. In June 1998,
we received net proceeds of $46.8 million from our initial public offering. We
raised an additional $2.0 million at the closing of our initial public offering
through the sale of common stock to America Online pursuant to a Common Stock
and Warrant Subscription Agreement entered into in March 1998. In May 1998, we
received $4.8 million through a credit agreement that we entered into with
Deutsche Bank AG. We repaid all monies borrowed under that credit agreement in
November 1998. In November and December 1998, we raised net cash proceeds
totaling approximately $63.3 million through the sale of our 7 1/4% Convertible
Subordinated Notes. On April 14, 1999, we completed the sale of 4,000,000 shares
of our common stock in a public offering, which generated net proceeds of $98.5
million.

     As of September 30, 1999, we had approximately $87.0 million of cash
compared with $81.5 million at September 30, 1998. Our current strategic
marketing alliances provide for remaining payments of approximately $8.3 million
in 1999, approximately $19.3 million in 2000 and approximately $7.8 million in
2001. Currently, we have no other material commitments other than those under
our operating leases and the U.S. government contracts.

     We used net cash of $81.9 million in operating activities in the nine
months ended September 30, 1999. Our cash used in operating activities in the
nine months ended September 30, 1999 was primarily comprised of the net effect
of:

     - a net loss of $90.8 million;

     - an increase in prepaid expense and other assets totaling $12.4 million
       related to advertising;
                                       13
<PAGE>   14

     - an increase in accounts receivable totaling $4.0 million related to
       invoiced government contract revenues;

     - an increase in accounts payable totaling $3.3 million related to costs
       associated with our U.S. government contracts, and

     - a non-cash charge of $25.1 million related to the amortization of
       deferred compensation and other intangible assets.

     We used net cash in investing activities in the nine months ended September
30, 1999 of $70.2 million for acquisitions of leasehold improvements and
computer equipment, investments in short-term securities, as well as costs
associated with the acquisition of BuyDirect.com.

     We received net cash of $99.6 million in the nine months ended September
30, 1999 from financing activities, primarily from proceeds of our secondary
public offering of our common stock and the exercise of stock options.

     We believe that our cash at September 30, 1999 will be sufficient to meet
our anticipated needs for working capital and capital expenditures for at least
the next 11 months. Thereafter, we expect that the cash we generate from
operations likely will not be sufficient to satisfy our cash needs. We will need
significant amounts of cash to make a variety of payments, including:

     - payment of the principal and interest on 7 1/4% Convertible Subordinated
       Notes when due;

     - payment of our financial obligations to America Online, Network
       Associates, Excite@Home, Yahoo!, CNET, XOOM, ZDNet and others; and

     - payment of increasing sales and marketing expenses.

     We may need to sell additional equity or debt securities to raise cash to
meet these obligations. Such sales likely would result in additional dilution to
our stockholders. In addition, we cannot assure you that financing will be
available in amounts or on terms acceptable to us, if at all.

YEAR 2000 RISK MAY ADVERSELY AFFECT OUR COMPANY

     Many existing computer programs use only two digits to identify a year.
These programs were designed and developed without addressing the impact of the
upcoming change in the century. If not corrected, many computer software
applications could fail or create erroneous results by, at or beyond the Year
2000. We assessed our proprietary software and our internally developed systems,
which permit the sale, order, processing and delivery of off-the-shelf software
to our customers to determine Year 2000 compliance. We searched through software
code for each of these applications and believe that we have identified all
instances where date specific information is required. We further investigated
whether these date fields contain two or four digits. Based on our review and
the results of limited testing, we believe our other proprietary software and
internally developed systems are Year 2000 compliant.

     In addition to our proprietary software and internally developed systems,
we utilize software, computer technology and other services internally developed
and provided by third-party vendors that may fail due to the Year 2000
phenomenon. For example, we are dependent on the institutions involved in
processing our members' credit card payments for Internet services. We are also
dependent on telecommunications vendors and leased point-of-purchase vendors to
maintain network reliability.

     Our software applications run on several hardware platforms and associated
operating systems, primarily those provided by Sun Microsystems. In addition,
our software operates in accordance with several external Internet protocols,
such as HTTP and NNTP. Our software is therefore dependent upon the correct
processing of dates by these systems and protocols. We reviewed information made
publicly available by Sun Microsystems and our other hardware platform providers
regarding Year 2000 compliance and researched the date handling capabilities of
applicable Internet protocols. Based on this research, we do not believe that
the underlying systems and protocols that operate in conjunction with our
software applications contain material Year 2000 deficiencies. We are currently
in the process of conducting our own tests to determine to what
                                       14
<PAGE>   15

extent our software running on any of our hardware platforms and in accordance
with any of our supported Internet protocols fails to properly recognize Year
2000 dates.

     We use multiple software systems for our internal business purposes,
including accounting, e-mail, development, human resources, customer service and
support, and sales tracking systems. All of these applications have been
purchased within the preceding 12 months. We have made inquiries of vendors of
the systems that we believe are mission critical to our business regarding their
Year 2000 readiness. Each of these vendors has indicated to us that it believes
its applications are Year 2000 compliant. We have received affirmative
documentation in this regard from many of these vendors, however, we have not
performed any operational tests on these internal systems. Based on our vendors
representation, we anticipate that our systems, including components thereof
provided by third-party vendors, will be Year 2000 compliant by the Year 2000.

     However, our software applications and the underlying hardware systems and
protocols running the software may contain undetected errors or defects
associated with Year 2000 date functions. Our software applications directly and
indirectly interact with a large number of other hardware and software systems.
We are unable to predict to what extent our business may be affected if our
software or the systems that operate in conjunction with our software experience
a material Year 2000 failure. Known or unknown errors or defects that affect the
operation of our software could result in delay or loss of revenue, interruption
of shopping services, cancellation of customer contracts, interference with
digital download, diversion of development resources, damage to our reputation,
costs, and litigation costs, any of which could adversely affect our business,
financial condition and results of operation. Further, the spending and
purchasing patterns of customers or potential customers may be affected by the
Year 2000 issue as individuals, corporations and government agencies expend
significant resources to correct or update their current systems for Year 2000
compliance or delay purchases of new software until after the Year 2000. We are
establishing contingency plans to handle the most reasonably likely worst case
scenarios.

                           PART II. OTHER INFORMATION

ITEM 1. LEGAL PROCEEDINGS -- NOT APPLICABLE

ITEM 2. CHANGES IN SECURITIES -- NOT APPLICABLE

ITEM 3. DEFAULTS UPON SENIOR SECURITIES -- NOT APPLICABLE

ITEM 4. SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS -- NOT APPLICABLE

ITEM 5. OTHER INFORMATION -- NOT APPLICABLE

ITEM 6. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

     We are exposed to the impact of interest rate changes, foreign currency
fluctuations, and change in the market values of our investments.

     Interest Rate Risk. Our exposure to market rate risk for changes in
interest rates relates primarily to our investment portfolio. We have not used
derivative financial instruments in our investment portfolio. We invest our
excess cash in debt instruments of the U.S. Government and its agencies, and in
high-quality corporate issuers and, by policy, limit the amount of credit
exposure to any one issuer. We protect and preserve our invested funds by
limiting default, market and reinvestment risk. Investments in both fixed rate
and floating rate interest earning instruments carry a degree of interest rate
risk. Fixed rate securities may have their fair market value adversely impacted
due to a rise in interest rates, while floating rate securities may produce less
income than expected if interest rates fall. Due in part to these factors, our
future investment income may fall short of expectations due to changes in
interest rates. We may suffer losses in principal if forced to sell securities
which have declined in market value due to changes in interest rates.

     Foreign Currency Risk. To date we have not experienced risks associated
with foreign currencies as a result of our operations. However, we intend to
expand internationally and will be exposed to risks associated with fluctuations
in foreign currencies at such time.

                                       15
<PAGE>   16

     Investment Risk. To date, we have not invested in equity instruments of
companies.

ITEM 7. EXHIBITS, FINANCIAL STATEMENT SCHEDULES, AND REPORTS ON FORM 8-K

(a) EXHIBITS

<TABLE>
<CAPTION>
    EXHIBIT
    NUMBER                            DESCRIPTION
    -------                           -----------
    <C>       <S>
    10.1*+    Contract dated June 16, 1999 between registrant and
              Intellisys Technology Corporation
    10.2*     Amended and Restated Electronic Software Reseller/Website
              Services Agreement dated May 17, 1999, between Beyond.com
              Corporation and Network Associates, Inc.
     27.1     Financial Data Schedule
</TABLE>

------------------------
* Confidential treatment has been requested as to certain portions of this
  exhibit.
+ To be filed by amendment.

(b) REPORTS ON FORM 8-K

     None.

                                       16
<PAGE>   17

                                   SIGNATURES

     Pursuant to the requirements of Section 13 or 15(d) of the Securities
Exchange Act of 1934, as amended, the registrant has duly caused this quarterly
report on Form 10-Q to be signed on its behalf by the undersigned, thereunto
duly authorized, in Sunnyvale, California, on August 16, 1999.

                                          BEYOND.COM CORPORATION

                                          By       /s/ MARK L. BREIER
                                            ------------------------------------
                                                       Mark L. Breier
                                             President, Chief Executive Officer
                                                        and Director

                                          By      /s/ GREGORY B. KELLEY
                                            ------------------------------------
                                                     Gregory B. Kelley
                                              Interim Chief Financial Officer

                                       17
<PAGE>   18

                               INDEX TO EXHIBITS

<TABLE>
<CAPTION>
EXHIBIT
NUMBER                            DESCRIPTION
-------                           -----------
<C>       <S>
10.1*+    Contract dated June 16, 1999 between registrant and
          Intellisys Technology Corporation
10.2*     Amended and Restated Electronic Software Reseller/Website
          Services Agreement dated May 17, 1999, between Beyond.com
          Corporation and Network Associates, Inc.
 27.1     Financial Data Schedule
</TABLE>

------------------------
* Confidential treatment has been requested as to certain portions of this
  exhibit.
+ To be filed by amendment.