<PAGE>

                      SECURITIES AND EXCHANGE COMMISSION
                            WASHINGTON, D.C. 20549

                                 FORM 10-K/A
                              Amendment No. 1
(MARK ONE)

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

     For the fiscal year ended December 31, 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  000-20364

                          BANYAN SYSTEMS INCORPORATED
            (Exact Name of Registrant as Specified in Its Charter)



                                 MASSACHUSETTS

        (State or Other Jurisdiction of Incorporation or Organization)



                                  04-2798394

                     (I.R.S. Employer Identification No.)




                               120 FLANDERS ROAD
                         WESTBORO, MASSACHUSETTS 01581
             (Address and Zip Code of Principal Executive Offices)

Registrant's telephone number, including area code: 508-898-1000

Securities registered pursuant to Section 12(b) of the Act: NONE

Securities registered pursuant to Section 12(g) of the Act:

                         COMMON STOCK, $.01 PAR VALUE
                               (Title of Class)

     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 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   [_]

     Indicate by check mark if disclosure of delinquent filers pursuant to Item
405 of Regulation S-K is not contained herein, and will not be contained, to the
best of Registrant's knowledge, in definitive proxy or information statements
incorporated by reference in Part III of this Form 10-K or any amendment to this
Form 10-K.     [_]

     The aggregate market value of the voting common stock held by non-
affiliates of the Registrant, based on a per share fair market value as of March
24, 2000 of $19.56, was approximately $386,933,318.52. For this purpose, any
officer, director or 5% stockholder of the Company is deemed to be an affiliate.
The Registrant has no shares of non-voting Common Stock authorized or
outstanding.

     On March 24, 2000, there were 23,320,488 shares of Common Stock
outstanding.

                      DOCUMENTS INCORPORATED BY REFERENCE

(1)  Specifically identified portions of the Annual Report to Shareholders for
     the fiscal year ended December 31, 1999 (the "Annual Report to
     Shareholders") are incorporated by reference into Parts I and II of this
     Annual Report on Form 10-K.

(2)  Specifically identified portions of the Company's Definitive Proxy
     Statement, to be filed with the Securities and Exchange Commission within
     120 days after December 31, 1999 in connection with the Company's 2000
     Annual Meeting of Stockholders, are incorporated by reference into Part III
     of this Annual Report on Form 10-K.


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                               EXPLANATORY NOTE

     The Annual Report on  Form 10-K of Banyan Systems Incorporated for the
fiscal year ended December 31, 1999, as filed with the Securities and Exchange
Commission on March 30, 2000, is hereby amended to (i) file Exhibit 10.4
thereto and (ii) refile Exhibit 23 thereto, which such Exhibit 23 is amended and
restated as filed herewith.


                                    PART IV

ITEM 14.  EXHIBITS, FINANCIAL STATEMENT SCHEDULES, AND REPORTS ON FORM 8-K

(a)  The following documents are filed as part of or are included in this Annual
     Report on Form 10-K:

     1.   Financial Statements:

          .    Consolidated Balance Sheets as of December 31, 1999 and 1998.

          .    Consolidated Statements of Operations for the years ended
               December 31, 1999, 1998, and 1997.

          .    Consolidated Statements of Shareholders' Equity for the years
               ended December 31, 1999, 1998 and 1997.

          .    Consolidated Statements of Cash Flows for the years ended
               December 31, 1999, 1998 and 1997.

          .    Notes to Consolidated Financial Statements.

          .    Report of Independent Accountants for the years ended December
               31, 1999, 1998 and 1997.

          .    Selected Financial Data for the years ended December 31, 1999,
               1998, 1997, 1996, and 1995.

     2.   Financial Statement Schedules:

          .    Report of Independent Accountants for the years ended December
               31, 1999, 1998 and 1997.

          .    Schedule II--Valuation and Qualifying Accounts.

          .    Schedules other than the one listed above have been omitted since
               they are either not required, not applicable or the information
               is otherwise included.

     3.   Listing of Exhibits:

          .    The Exhibits filed as part of this Annual Report on Form 10-K are
               listed in the Exhibit Index immediately preceding such Exhibits,
               which Exhibit Index is incorporated herein by reference.
               Documents listed on such Exhibit Index, except for documents
               identified by footnotes, are being filed as exhibits herewith.
               Documents identified by footnotes are not being filed herewith
               and, pursuant to Rule 12b-32 under the Securities Exchange Act of
               1934, reference is made to such documents as previously filed
               with the Securities and Exchange Commission. The Registrant's
               file number under the Securities Exchange Act of 1934 is
               000-20364.

     (b)  No reports on Form 8-K were filed by the Registrant during the last
          quarter of the fiscal year ended December 31, 1999.


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                                 SIGNATURE

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange
Act of 1934, the Registrant has duly caused this report to be signed on its
behalf by the undersigned, thereunto duly authorized.

Dated: April 5, 2000     BANYAN SYSTEMS INCORPORATED


                           /s/ Richard M. Spaulding
                          -------------------------
                          By: Richard M. Spaulding
                          Senior Vice President and Chief Financial Officer

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                                 EXHIBIT INDEX

<TABLE>
<CAPTION>
    EXHIBIT
---------------  ---------------------------------------------------------------------------------------------------
    NUMBER                                                TITLE OF DOCUMENT
---------------  ---------------------------------------------------------------------------------------------------
<S>              <C>
 3.1(2)          Second Amended and Restated Articles of Organization of the Registrant.

 3.1A(7)         Certificate of Vote of Directors Establishing a Class or Series of Stock

 3.2(1)          Amended and Restated By-Laws of the Registrant.

 3.2A**          Amendment No. 1 to Amended and Restated By-Laws of the Registrant.

10.1+(8)         Second Amended and Restated 1984 Incentive Stock Option Plan.

10.2+(8)         Second Amended and Restated 1984 Non-Qualified Stock Option Plan.

10.3+(11)        1992 Stock Incentive Plan, as amended.

10.3A+(11)       Form of Incentive Stock Option for grant under the Registrant's 1992 Stock Incentive Plan, as
                 amended.

10.3B+(11)       Form of Non-Qualified Stock Option for grant under the Registrant's 1992 Stock Incentive Plan, as
                 amended.

10.4+            1992 Director Stock Option Plan, as amended.

10.5             Reserved.

10.6+(4)(5)      Employment Agreement dated February 4, 1997 between the Registrant and William P. Ferry, as
                 amended.

10.6A+(10)       Amendment No. 2 dated as of October 16, 1998 to Employment Agreement between the Registrant
                 and William P. Ferry.

10.6B+**         Amendment No. 3 dated as of December 8, 1999 to Employment Agreement between the Registrant and
                 William P. Ferry.

10.7(1)          Real Estate Sublease dated June 19, 1991, as amended to date, between the Registrant and Sytron
                 Corporation.

10.8(1)          Lease Agreement dated April 21, 1989, as amended to date, between the Registrant and CB
                 Westboro C Limited Partnership, a Texas Limited Partnership.
</TABLE>


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<TABLE>
<CAPTION>
    EXHIBIT
---------------  ---------------------------------------------------------------------------------------------------
    NUMBER                                                TITLE OF DOCUMENT
---------------  ---------------------------------------------------------------------------------------------------
<S>              <C>
10.8A(10)        Amendment to Lease Agreement dated April 21, 1993 between the Registrant and CB Westboro C
                 Limited Partnership, a Texas Limited Partnership.

10.8B(3)         Amendment to Lease Agreement dated April 21, 1993 between the Registrant and Commonwealth
                 Westboro Limited Partnership, a Massachusetts Limited Partnership (as successor in interest to CB
                 Westboro C Limited Partnership, a Texas Limited Partnership).

10.9(1)(10)      Lease Agreement dated November 14, 1986, as amended to date, between the Registrant and Aetna
                 Real Estate Associated, L.P. (as assignee of Flanders Realty Trust).

10.9A(10)        Amendment to Lease Agreement dated April 1, 1993 between the Registrant and Aetna Real Estate,
                 L.P. (as assignee of Flanders Realty Trust).

10.9B(8)         Fifth Lease Extension and Modification Agreement made as of October 15, 1997 between Aetna
                 Real Estate Associates and the Registrant.

10.10(6)         Loan and Security Agreement dated as of September 4, 1997 by and between Foothill Capital
                 Corporation and the Registrant.

10.10A(8)        Consent and Amendment to Loan and Security Agreement dated as of March 5, 1998 by and
                 between Foothill Capital Corporation and the Regisrant.

10.11(6)         Securities Issuance Agreement dated as of September 4, 1997 by and between Foothill Capital
                 Corporation and the Registrant.

10.12(6)         Form of Warrant issued by and to be issued by the Registrant to Foothill Capital Corporation.

10.13(7)         Preferred Stock and Warrant Purchase Agreement dated as of March 5, 1998 between the Registrant
                 and HarbourVest Partners V--Direct Fund L.P. ("HarbourVest").
</TABLE>
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<TABLE>
<CAPTION>
      EXHIBIT
-------------------  ----------------------------------------------------------------------------------------------
      NUMBER                                               TITLE OF DOCUMENT
-------------------  ----------------------------------------------------------------------------------------------
<S>                  <C>
10.14(7)             Warrant to purchase shares of Series B Convertible Preferred Stock issued by the Registrant to
                     HarbourVest as of March 5, 1998.

10.15(7)             Warrant to purchase shares of Series C Convertible Preferred Stock issued by the Regisrant to
                     HarbourVest as of March 5, 1998.

10.16+(8)(9)         Separation Agreement and Release and Waiver of Claims dated as of May 31, 1997 between
                     the Registrant and David C. Mahoney, as amended.

10.17+(10)           Executive Retention Agreement dated as of October 16, 1998 between the Registrant and
                     Robert D. Burke.

10.18+(10)           Executive Retention Agreement dated as of October 16, 1998 between the Registrant and
                     Richard M. Spaulding.

10.19+(10)           Executive Retention Agreement dated as of October 16, 1998 between the Registrant and
                     Anthony J. Bellantuoni.

10.20+(10)           Executive Officer Restricted Stock Agreement dated October 16, 1998 between the Registrant
                     and William P. Ferry.

10.21+(10)           Executive Officer restricted Stock Agreement dated October 16, 1998 between the Registrant
                     and Robert D. Burke.

10.22+(10)           Executive Officer Restricted Stock Agreement dated October 16, 1998 between the Registrant
                     and Richard M. Spaulding.

10.23+(10)           Executive Officer Restricted Stock Agreement dated October 16, 1998 between the Registrant
                     and Anthony J. Bellantuoni.

10.24*(12)           Alliance Agreement dated January 8, 1999 between the Registrant and Microsoft Corporation.

10.25(12)            Warrant Purchase Agreement January 8, 1999 between the Registrant and Microsoft.

10.26(12)            Common Stock Purchase Warrant issued by the Registrant to Microsoft on January 8, 1999.

10.27+(12)           Employment Letter dated as of January 15, 1999 between the Registrant and Scott G. Silk.

10.28+(12)           Non-Qualified Stock Option Agreement dated February 4, 1997 granted by the Registrant to
                     William P. Ferry.

10.29+(12)           Non-Qualified Stock Option Agreement dated March 20, 1997 granted by the Registrant to
                     Robert D. Burke.
</TABLE>
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<TABLE>
<CAPTION>
      EXHIBIT
-------------------  ----------------------------------------------------------------------------------------------
      NUMBER                                               TITLE OF DOCUMENT
-------------------  ----------------------------------------------------------------------------------------------
<S>                  <C>
10.30+(12)           Non-Qualified Stock Option Agreement dated June 11, 1997 granted by the Registrant to Anthony
                     J. Bellantuoni.

10.31(13)            Common Stock and Warrant Purchase Agreement dated as of June 1, 1999 by and among Switchboard
                     Incorporated, the Registrant and CBS Corporation, as amended.

10.31A(14)           Amendment No. 2 to Common Stock and Warrant Purchase Agreement by and among Switchboard
                     Incorporated, the Registrant and CBS Corporation, effective as of July 1, 1999.

10.32*(13)           Common Stock Purchase Warrant issued by Switchboard Incorporated to CBS Corporation on June
                     30, 1999.

10.33*(13)            Advertising and Promotion Agreement dated as of June 30, 1999 by and among CBS Corporation,
                     the Registrant and Switchboard Incorporated.

10.34(13)            License Agreement dated as of June 30, 1999 by and between CBS Corporation and Switchboard
                     Incorporated.

10.35(13)            Warrant Purchase Agreement dated as of June 1, 1999 by and between the Company and CBS
                     Corporation.

10.36(13)            Common Stock Purchase Warrant issued by the Registrant to CBS Corporation on June 30, 1999.

10.37+**             Non-Qualified Stock Option Agreement dated October 21, 1999 granted by the Registrant to
                     William P. Ferry.

10.38+**             Non-Qualified Stock Option Agreement dated December 8, 1999 granted by the Registrant to
                     William P. Ferry.

10.39+**             Executive Officer restricted stock Agreement dated October 8, 1999 between the Registrant and
                     Scott G. Silk.

13**                 Selected portions of the Registrant's Annual Report to Shareholders for the year ended
                     December 31, 1999 (which is not deemed to be "filed" except to the extent that portions
                     thereof are expressly incorporated by reference in this Annual Report on Form 10-K).

21**                 Subsidiaries of the Company.

23***                Consent of PricewaterhouseCoopers LLP.

27**                 Financial Data Schedule.
</TABLE>

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----------------
+    Management contract or compensation plan or arrangement required to be
     filed as an exhibit pursuant to Item 14(c) of Form 10-K.

*    Confidential treatment has been requested as to certain portions, which
     portions have been omitted and filed seperately with the Securities and
     Exchange Commission.

**   Previously filed.

***  Superseding exhibit.

(1)  Incorporated herein by reference to the exhibits to the Registrant's
     Registration statement on Form S-1 (File No. 33-49194).

(2)  Incorporated herein by reference to the exhibits to the Registrant's
     Registration statement on Form S-8 (File No. 33-54140).

(3)  Incorporated herein by reference to the exhibits to the Registrant's
     Quarterly Report on Form 10-Q for the fiscal quarter ended September 30,
     1995.

(4)  Incorporated herein by reference to the exhibits to the Registrant's Annual
     Report on Form 10-K for the fiscal year ended December 31, 1996.

(5)  Incorporated herein by reference to the exhibits to the Registrant's
     Quarterly Report on Form 10-Q for the fiscal quarter ended June 30, 1997.

(6)  Incorporated herein by reference to the exhibits to the Registrant's
     Quarterly Report on Form 10-Q for the fiscal quarter ended September 30,
     1997.

(7)  Incorporated herein by reference to the exhibits to the Registrant's
     Current Report on Form 8-K dated March 5, 1998.

(8)  Incorporated herein by reference to the exhibits to the Registrant's Annual
     Report on Form 10-K for the fiscal year ended December 31, 1997.

(9)  Incorporated herein by reference to the exhibits to the Registrant's
     Quarterly Report on Form 10-Q for the fiscal quarter ended September 30,
     1998.

(10) Incorporated herein by reference to the exhibits to the Registrant's Annual
     Report on Form 10-K for the fiscal year ended December 31, 1998.

(11) Incorporated herein by reference to the exhibits to the Company's
     Registration Statement on Form S-8 (File No. 333-70553).

(12) Incorporated herein by reference to the exhibits to the Registrant's
     Quarterly Report on Form 10-Q for the fiscal   quarter ended March 31,
     1999.

(13) Incorporated herein by reference to the exhibits to the Registrant's
     Quarterly Report on Form 10-Q for the fiscal quarter ended June 30, 1999.

(14) Incorporated herein by reference to Exhibit 10.4A to Switchboard
     Incorporated's Registration Statement on Form S-1 (Commission File No. 333-
     90013), filed on October 29, 1999, as amended.