<PAGE>

                                 UNITED STATES
                      SECURITIES AND EXCHANGE COMMISSION
                            Washington, D. C. 20549

                                  FORM 10-K/A
                                Amendment No. 2
(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, 1998
                                          ------------------------

                                 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  0-20017

                           CNL INCOME FUND IX, LTD.
            (Exact name of registrant as specified in its charter)

            Florida                                 59-3004138
(State or other jurisdiction of        (I.R.S. Employer Identification No.)
 incorporation or organization)

                            450 South Orange Avenue
                            Orlando, Florida 32801
         (Address of principal executive offices, including zip code)

      Registrant's telephone number, including area code: (407) 650-1000

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

      Title of each class:          Name of exchange on which registered:
              None                              Not Applicable

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

             Units of limited partnership interest ($10 per Unit)
                               (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 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. [X]

     Aggregate market value of the voting stock held by nonaffiliates of the
registrant: The registrant registered an offering of 3,500,000 units of limited
partnership interest (the "Units") on Form S-11 under the Securities Act of
1933, as amended. Since no established market for such Units exists, there is no
market value for such Units. Each Unit was originally sold at $10 per Unit.

                     DOCUMENTS INCORPORATED BY REFERENCE:
                                     None
<PAGE>

     The Form 10-K of CNL Income Fund IX, Ltd. for the year ended December 31,
1998 is being amended to revise the disclosure under Item 1. Business.


                                 PART I

Item 1.  Business

         CNL Income Fund IX, Ltd. (the "Registrant" or the "Partnership") is a
limited partnership which was organized pursuant to the laws of the State of
Florida on April 16, 1990. The general partners of the Partnership are Robert A.
Bourne, James M. Seneff, Jr. and CNL Realty Corporation, a Florida corporation
(the "General Partners"). Beginning on March 20, 1991, the Partnership offered
for sale up to $35,000,000 in limited partnership interests (the "Units")
(3,500,000 Units each at $10 per Unit) pursuant to a registration statement on
Form S-11 under the Securities Act of 1933, as amended. The offering terminated
on September 6, 1991, at which date the maximum offering proceeds of $35,000,000
had been received from investors who were admitted to the Partnership as limited
partners (the "Limited Partners").

         The Partnership was organized to acquire both newly constructed and
existing restaurant properties, as well as properties upon which restaurants
were to be constructed (the "Properties"), which are leased primarily to
operators of national and regional fast-food and family-style restaurant chains
(the "Restaurant Chains"). Net proceeds to the Partnership from its offering of
Units, after deduction of organizational and offering expenses, totalled
$30,800,000, and were used to acquire 41 Properties, including 13 Properties
owned by joint ventures in which the Partnership is a co-venturer, and to
establish a working capital reserve for Partnership purposes. During the year
ended December 31, 1997, the Partnership sold its Property in Alpharetta,
Georgia, and reinvested the net sales proceeds in an IHOP Property located in
Englewood, Colorado, with an affiliate of the General Partners, as tenants-in-
common. As a result of the above transactions, as of December 31, 1998, the
Partnership owned 41 Properties. The 41 Properties include 13 Properties owned
by joint ventures in which the Partnership is a co-venturer and one Property
owned with an affiliate as tenants-in-common. In February and March 1999, the
Partnership sold two Properties, one in Corpus Christi, Texas and one in
Rochester, New York, respectively. The Partnership intends to reinvest the net
sales proceeds from these sales in additional Properties. The Partnership leases
the Properties on a triple-net basis with the lessees responsible for all
repairs and maintenance, property taxes, insurance and utilities.

         On March 11, 1999, the Partnership entered into an Agreement and Plan
of Merger with CNL American Properties Fund, Inc. ("APF"), pursuant to which the
Partnership would be merged with and into a subsidiary of APF (the "Merger").
APF is a real estate investment trust whose primary business is the ownership of
restaurant properties leased on a long-term, "triple-net" basis to operators of
national and regional restaurant chains. APF has agreed to issue shares of its
common stock, par value $0.01 per share (the "APF Shares"), as consideration for
the Merger. At a special meeting of the partners that is expected to be held in
the fourth quarter of 1999, Limited Partners holding in excess of 50% of the
Partnership's outstanding limited partnership interests must approve the Merger
prior to consummation of the transaction. If the Limited Partners at the special
meeting approve the Merger, APF will own the Properties and other assets of the
Partnership.

         In the event that the Limited Partners vote against the Merger, the
Partnership will hold its Properties until the General Partners determine that
the sale or other disposition of the Properties is advantageous in view of the
Partnership's investment objectives. In deciding whether to sell Properties, the
General Partners will consider factors such as potential capital appreciation,
net cash flow and federal income tax considerations. Certain lessees also have
been granted options to purchase Properties, generally at the Property's then
fair market value after a specified portion of the lease term has elapsed. The
Partnership has no obligation to sell all or any portion of a Property at any
particular time, except as may be required under property purchase options
granted to certain lessees.
<PAGE>

Leases

     Although there are variations in the specific terms of the leases, the
following is a summarized description of the general structure of the
Partnership's leases.  The leases of the Properties owned by the Partnership,
the joint ventures in which the Partnership is a co-venturer and the Properties
owned with affiliates as tenants-in-common, generally provide for initial terms
ranging from 10 to 20 years (the average being 17 years), and expire between
2005 and 2017.  The leases are on a triple-net basis, with the lessees
responsible for all repairs and maintenance, property taxes, insurance and
utilities.  The leases of the Properties provide for minimum base annual rental
payments (payable in monthly installments) ranging from approximately $51,500 to
$171,400.  In addition, generally the leases provide for percentage rent, based
on sales in excess of a specified amount.  In addition, a majority of the leases
provide that, commencing in specified lease years (ranging from the third to the
sixth lease year), the annual base rent required under the terms of the lease
will increase.

     Generally, the leases of the Properties provide for two to five five-year
renewal options subject to the same terms and conditions as the initial lease.
Lessees of 28 of the Partnership's 41 Properties also have been granted options
to purchase Properties at the Property's then fair market value after a
specified portion of the lease term has elapsed.  Fair market value will be
determined through an appraisal by an independent appraisal firm.  Under the
terms of certain leases, the option purchase price may equal the Partnership's
original cost to purchase the Property (including acquisition costs), plus a
specified percentage from the date of the lease or a specified percentage of the
Partnership's purchase price, if that amount is greater than the Property's fair
market value at the time the purchase option is exercised.

     The leases also generally provide that, in the event the Partnership wishes
to sell the Property subject to that lease, the Partnership first must offer the
lessee the right to purchase the Property on the same terms and conditions, and
for the same price, as any offer which the Partnership has received for the sale
of the Property.

     During 1998, a tenant, Brambury Associates filed for bankruptcy and
rejected the lease relating to one of their two leases and ceased making rental
payments to the Partnership on the rejected lease.  The Partnership will not
recognize rental and earned income from this Property until a new tenant is
located or until the Property is sold and the proceeds from such sale are
reinvested in an additional Property.  The lost revenues resulting from the
lease that was rejected could have an adverse effect on the results of
operations of the Partnership if the Partnership is unable to re-lease the
Property in a timely manner.  The General Partners are currently seeking either
a new tenant or purchaser for the Property with the rejected lease.  The
Partnership continued receiving rental payments on the lease that was not
rejected and in March 1999, the Partnership sold this Property to a third party.
The Partnership intends to reinvest the net sales proceeds in an additional
Property.

     During 1998, four of the Partnership's leases, were amended to provide for
rent reductions from August 1998 through the end of the lease term.  However,
the General Partners do not anticipate that any decrease in rental income due to
these rent reductions relating to the Properties will have a material effect on
the Partnership's financial position or results of operations.

     During 1994, the leases relating to the Properties in Blufton, Alliance and
North Baltimore, Ohio were amended to provide for the payment of reduced annual
base rent with no scheduled rent increases.  However, the lease amendment
provided for lower percentage rent breakpoints, as compared to the original
lease agreement, a change that was designed to result in higher percentage rent
payments at any time that percentage rent became payable.  In accordance with a
provision in the amendments, as a result of the former tenant assigning the
leases to a new tenant during 1998, the rents under the assigned lease reverted
back to those that were required under the original lease agreements.

Major Tenants

     During 1998, five of the Partnership's lessees (or group of affiliated
lessees), (i) Carrols Corporation, (ii) TPI Restaurants, Inc., (iii) Flagstar
Enterprises, Inc., (iv) Burger King Corporation and BK Acquisition, Inc. (which
are affiliated entities under common control) (hereinafter referred to as Burger
King Corp.) and (v) Golden Corral Corporation, each contributed more than ten
percent of the Partnership's total rental income (including the Partnership's
<PAGE>

share of rental income from 13 Properties owned by joint ventures and one
Property owned as tenants-in-common). As of December 31, 1998, Carrols
Corporation was the lessee under leases relating to four restaurants, TPI
Restaurants, Inc. was the lessee under leases relating to five restaurants,
Flagstar Enterprises, Inc. was the lessee under leases relating to five
restaurants, Burger King Corp. was the lessee under leases relating to the 13
restaurants owned by joint ventures and Golden Corral Corporation was the lessee
under leases relating to two restaurants. It is anticipated that, based on the
minimum rental payments required by the leases, these five lessees or groups of
affiliated lessees each will continue to contribute more than ten percent of the
Partnership's total rental income in 1999. In addition, four Restaurant Chains,
Burger King, Hardee's, Shoney's and Golden Corral Family Steakhouse Restaurants
("Golden Corral"), each accounted for more than ten percent of the Partnership's
total rental income during 1998 (including the Partnership's share of the rental
income from 13 Properties owned by joint ventures and one Property owned as
tenants-in-common). In 1999, it is anticipated that these four Restaurant Chains
each will continue to account for more than ten percent of the total rental
income to which the Partnership is entitled under the terms of its leases. Any
failure of these lessees or Restaurant Chains could materially affect the
Partnership's income if the Partnership is not able to re-lease the Properties
in a timely manner. No single tenant or group of affiliated tenants lease
Properties with an aggregate carrying value in excess of 20 percent of the total
assets of the Partnership.

Joint Venture and Tenancy in Common Arrangements

     The Partnership has entered into the following separate joint venture
arrangements: CNL Restaurant Investments II with CNL Income Fund VII, Ltd. and
CNL Income Fund VIII, Ltd., affiliates of the General Partners, to purchase and
hold six Properties; CNL Restaurant Investments III with CNL Income Fund X,
Ltd., an affiliate of the General Partners, to purchase and hold six Properties;
and Ashland Joint Venture with CNL Income Fund X, Ltd. and CNL Income Fund XI,
Ltd., affiliates of the General Partners, to purchase and hold one Property.
Each of the affiliates is a limited partnership organized pursuant to the laws
of the State of Florida.

     The joint venture arrangements provide for the Partnership and its joint
venture partners to share in all costs and benefits associated with the joint
ventures in accordance with their respective percentage interests in the joint
ventures. The Partnership has a 45.2% interest in CNL Restaurant Investments II,
a 50 percent interest in CNL Restaurant Investments III and a 27.33% interest in
Ashland Joint Venture. The Partnership and its joint venture partners are also
jointly and severally liable for all debts, obligations and other liabilities of
the joint ventures.

     CNL Restaurant Investments II's and CNL Restaurant Investments III's joint
venture agreements do not provide a fixed term, but continue in existence until
terminated by any of the joint venturers. Ashland Joint Venture has an initial
term of 30 years and, after the expiration of the initial term, continues in
existence from year to year unless terminated at the option of any of the joint
venturers or by an event of dissolution. Events of dissolution include the
bankruptcy, insolvency or termination of any joint venturer, sale of the
Property owned by the joint venture and mutual agreement of the Partnership and
its joint venture partners to dissolve the joint venture.

     The joint venture agreements restrict each venturer's ability to sell,
transfer or assign its joint venture interest without first offering it for sale
to its joint venture partners, either upon such terms and conditions as to which
the venturers may agree or, in the event the venturers cannot agree, on the same
terms and conditions as any offer from a third party to purchase such joint
venture interest.

     Net cash flow from operations of CNL Restaurant Investments II, CNL
Restaurant Investments III and Ashland Joint Venture is distributed 45.2%, 50
percent and 27.33%, respectively, to the Partnership and the balance is
distributed to each of the other joint venture partners in accordance with their
respective percentage interest in the joint venture. Any liquidation proceeds,
after paying joint venture debts and liabilities and funding reserves for
contingent liabilities, will be distributed first to the joint venture partners
with positive capital account balances in proportion to such balances until such
balances equal zero, and thereafter in proportion to each joint venture
partner's percentage interest in the joint venture.

     In addition to the above joint venture arrangements, in July 1997, the
Partnership entered into an agreement to hold an IHOP Property as
tenants-in-common, with CNL Income Fund III, Ltd., an affiliate of the General
Partners. The agreement provides for the Partnership and the affiliate to share
in the profits and losses of the Property in proportion to each co-tenant's
percentage interest. The Partnership owns a 67 percent interest in this
Property. The
<PAGE>

affiliate is a limited partnership organized pursuant to the laws of the State
of Florida. The tenancy in common agreement restricts each co-tenant's ability
to sell, transfer, or assign its interest in the tenancy in common's Property
without first offering it for sale to the remaining co-tenant.

     The use of joint venture and tenancy in common arrangements allows the
Partnership to fully invest its available funds at times at which it would not
have sufficient funds to purchase an additional property, or at times when a
suitable opportunity to purchase an additional property is not available. The
use of joint venture and tenancy in common arrangements also provides the
Partnership with increased diversification of its portfolio among a greater
number of properties. In addition, tenancy in common arrangements may allow the
Partnership to defer the gain for federal income tax purposes upon the sale of
the property if the proceeds are reinvested in an additional property.

Certain Management Services

     CNL Fund Advisors, Inc., an affiliate of the General Partners, provides
certain services relating to management of the Partnership and its Properties
pursuant to a management agreement. Under this agreement, CNL Fund Advisors,
Inc. is responsible for collecting rental payments, inspecting the Properties
and the tenants' books and records, assisting the Partnership in responding to
tenant inquiries and notices and providing information to the Partnership about
the status of the leases and the Properties. CNL Fund Advisors, Inc. also
assists the General Partners in negotiating the leases. For these services, the
Partnership has agreed to pay CNL Fund Advisors, Inc. an annual fee of one
percent of the sum of gross rental revenues from Properties wholly owned by the
Partnership plus the Partnership's allocable share of gross revenues of joint
ventures in which the Partnership is a co-venturer, but not in excess of
competitive fees for comparable services. Under the management agreement, the
management fee is subordinated to receipt by the Limited Partners of an
aggregate, ten percent, cumulative, noncompounded annual return on their
adjusted capital contributions (the "10% Preferred Return"), calculated in
accordance with the Partnership's limited partnership agreement (the
"Partnership Agreement").

     The management agreement continues until the Partnership no longer owns an
interest in any Properties unless terminated at an earlier date upon 60 days'
prior notice by either party.

Employees

     The Partnership has no employees. The officers of CNL Realty Corporation
and the officers and employees of CNL Fund Advisors, Inc. perform certain
services for the Partnership. In addition, the General Partners have available
to them the resources and expertise of the officers and employees of CNL Group,
Inc., a diversified real estate company, and its affiliates, who may also
perform certain services for the Partnership.
<PAGE>

                                  SIGNATURES

     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, on the 17th day of
December, 1999.

                               CNL INCOME FUND IX, LTD.

                               By: CNL REALTY CORPORATION
                                   General Partner

                                   /s/ Robert A. Bourne
                                   ---------------------------
                                   ROBERT A. BOURNE, President


                               By: ROBERT A. BOURNE
                                   General Partner

                                   /s/ Robert A. Bourne
                                   ---------------------------
                                   ROBERT A. BOURNE


                               By: JAMES M. SENEFF, JR.
                                   General Partner

                                   /s/ James M. Seneff, Jr.
                                   ---------------------------
                                   JAMES M. SENEFF, JR.
<PAGE>

     Pursuant to the requirements of the Securities Exchange Act of 1934, this
report has been signed below by the following persons on behalf of the
Registrant and in the capacities and on the dates indicated.

<TABLE>
<CAPTION>

       Signature                                  Title                                      Date
       ---------                                  -----                                      ----
<S>                                     <C>                                             <C>
/s/ Robert A. Bourne                    President, Treasurer and Director               December 17, 1999
------------------------------------
Robert A. Bourne                        (Principal Financial and Accounting
                                        Officer)

/s/ James M. Seneff, Jr.                Chief Executive Officer and Director            December 17, 1999
------------------------------------
James M. Seneff, Jr.                    (Principal Executive Officer)
</TABLE>