<PAGE>
                                                                     Exhibit 3.2

                           CERTIFICATE OF AMENDMENT OF

                              AMENDED AND RESTATED

                          CERTIFICATE OF INCORPORATION

                                       OF

                           PERSISTENCE SOFTWARE, INC.


         The undersigned, Christopher T. Keene, hereby certifies that:

         1. He is the duly elected and acting Chief Executive Officer and
Secretary of Persistence Software, Inc., a Delaware corporation.

         2. The Certificate of Incorporation of this corporation was originally
filed with the Secretary of State of Delaware on April 28, 1999.

         3. Pursuant to Section 242 of the General Corporation Law of the State
of Delaware, this Certificate of Amendment amends and restates Article IV of
this corporation's Amended and Restated Certificate of Incorporation:


         "(A) CLASSES OF STOCK. The Corporation is authorized to issue two
         classes of stock to be designated, respectively, "Common Stock" and
         "Preferred Stock." The total number of shares which the Corporation is
         authorized to issue is Eight Million (8,000,000) shares, each with a
         par value of $0.001 per share. Seven Million Five Hundred Thousand
         (7,500,000) shares shall be Common Stock and Five Hundred Thousand
         (500,000) shares shall be Preferred Stock."

         4. The foregoing Certificate of Amendment has been duly adopted by this
corporation's Board of Directors and stockholders in accordance with the
applicable provisions of Section 242 of the General Corporation Law of the State
of Delaware.

<PAGE>

         This Certificate of Amendment is executed at San Mateo, California,
July 12, 2004.



                                          /S/ CHRISTOPHER T. KEENE
                                          -------------------------------------
                                          Christopher T. Keene
                                          Chief Executive Officer and Secretary

<PAGE>

                           CERTIFICATE OF AMENDMENT OF

                              AMENDED AND RESTATED

                          CERTIFICATE OF INCORPORATION

                                       OF

                           PERSISTENCE SOFTWARE, INC.


         The undersigned, Christopher Keene and Christine Russell, hereby
certify that:

         1. They are the duly elected and acting Chief Executive Officer and
Secretary, respectively, of Persistence Software, Inc., a Delaware corporation.

         2. The Certificate of Incorporation of this corporation was originally
filed with the Secretary of State of Delaware on April 28, 1999.

         3. Pursuant to Section 242 of the General Corporation Law of the State
of Delaware, this Certificate of Amendment adds the following paragraph to the
end of Article IV of this corporation's Amended and Restated Certificate of
Incorporation:

         "At 12:00 a.m. Eastern Standard Time on June 12, 2003 (the "EFFECTIVE
         DATE"), each one outstanding share of this corporation's Common Stock
         shall be converted and reconstituted into 1/10th of a share of this
         corporation's Common Stock (the "REVERSE SPLIT"). In lieu of issuing
         any fractional shares, each holder of Common Stock who would otherwise
         have been entitled to a fraction of a share upon surrender of such
         holder's certificate(s) will be entitled to receive a cash payment,
         without interest, determined by multiplying (i) the fractional share
         interest to which the holder would otherwise be entitled, after taking
         into account all shares of Common Stock then held on the record date by
         the holder, and (ii) the average closing sale price of shares of Common
         Stock for the 10 trading days immediately prior to the Effective Date
         (on a post-Reverse Split basis) or, if no such sale takes place on such
         days, the average of the closing bid and asked prices for such days, in
         each case as officially reported by Nasdaq. Shares of Common Stock that
         were outstanding prior to the Reverse Split, and that are not
         outstanding after and as a result of the Reverse Split, shall resume
         the status of authorized but unissued shares of Common Stock."

         4. The foregoing Certificate of Amendment has been duly adopted by this
corporation's Board of Directors and stockholders in accordance with the
applicable provisions of Section 242 of the General Corporation Law of the State
of Delaware.

<PAGE>

         This Certificate of Amendment is executed at San Mateo, California,
June 6, 2003.


                                                  /S/ CHRISTOPHER KEENE
                                                  ------------------------------
                                                  Christopher Keene
                                                  Chief Executive Officer


                                                  /S/ CHRISTINE RUSSELL
                                                  ------------------------------
                                                  Christine Russell
                                                  Secretary

<PAGE>

                              AMENDED AND RESTATED
                          CERTIFICATE OF INCORPORATION
                                       OF
                           PERSISTENCE SOFTWARE, INC.

         Christopher T. Keene and Christine Russell hereby certify that:

         1. The date of filing the original Certificate of Incorporation of this
corporation with the Secretary of State of the State of Delaware is April 28,
1999.

         2. They are the duly elected and acting Chief Executive Officer and
Secretary, respectively, of Persistence Software, Inc., a Delaware corporation.

         3. The Certificate of Incorporation of this corporation is hereby
amended and restated to read as follows:

                                    ARTICLE I

         "The name of this corporation is Persistence Software, Inc. (the
"CORPORATION").

                                   ARTICLE II

         The address of the registered office of the Corporation in the State of
Delaware is:

                           Corporation Trust Company
                           1209 Orange Street
                           Wilmington, County of New Castle
                           Delaware, 19801

         The name of the Corporation's registered agent at said address is The
Corporation Trust Company.

                                   ARTICLE III

         The purpose of the Corporation is to engage in any lawful act or
activity for which corporations may be organized under the General Corporation
Law of Delaware.

                                   ARTICLE IV

         (A) CLASSES OF STOCK. The Corporation is authorized to issue two
classes of stock to be designated, respectively, "COMMON STOCK" and "PREFERRED
STOCK." The total number of shares which the Corporation is authorized to issue
is 80,000,000 shares, each with a par value of $0.001 per share. 75,000,000 of
such shares shall be Common Stock, and 5,000,000 of such shares shall be
Preferred Stock.
<PAGE>

         (B) The Preferred Stock may be issued from time to time in one or more
series. The Board of Directors is hereby authorized, within the limitations and
restrictions stated in this Certificate of Incorporation, to determine or alter
the rights, preferences, privileges and restrictions granted to or imposed upon
any wholly unissued series of Preferred Stock and the number of shares
constituting any such series and the designation thereof, or any of them; and to
increase or decrease the number of shares of any series subsequent to the
issuance of shares of that series, but not below the number of shares of such
series then outstanding. In case the number of shares of any series shall be so
decreased, the shares constituting such decrease shall resume the status which
they had prior to the adoption of the resolution originally fixing the number of
shares of such series.

                                    ARTICLE V

         The number of directors of the Corporation shall be fixed from time to
time by a bylaw or amendment thereof duly adopted by the Board of Directors.

                                   ARTICLE VI

         "LISTING EVENT" as used in this Amended and Restated Certificate of
Incorporation shall mean the first annual meeting of stockholders following such
time as the Corporation meets the criteria set forth in subdivisions (1), (2) or
(3) of Section 2115(c) the California Corporations Code as of the record date of
such meeting.

         For the management of the business and for the conduct of the affairs
of the Corporation, and in further definition, limitation and regulation of the
powers of the Corporation, its directors and its stockholders or any class
thereof, as the case may be, it is further provided that, effective upon the
occurrence of the Listing Event:

                  (i) The number of directors which shall constitute the entire
Board of Directors, and the number of directors in each class, shall be fixed
exclusively by one or more resolutions adopted from time to time by the Board of
Directors. The Board of Directors shall be divided into three classes,
designated as Class I, Class II and Class III, respectively. Directors shall be
assigned to each class in accordance with a resolution or resolutions adopted by
the Board of Directors. Until changed by a resolution of the Board of Directors,
Class I shall consist of three directors, each of whom shall be designated by
the Board of Directors; Class II shall consist of three directors, each of whom
shall be designated by the Board of Directors; and Class III shall consist of
three directors, each of whom shall be designated by the Board of Directors.

                           Upon the occurrence of the Listing Event, the terms
of office of the Class I directors shall expire, and Class I directors shall be
elected for a full term of three years. At the first annual meeting of
stockholders following the Listing Event, the term of office of the Class II
directors shall expire, and Class II directors shall be elected for a full term
of three years. At the second annual meeting of stockholders following the
Listing Event, the term of office of the Class III directors shall expire, and
Class III directors shall be elected for a full term of three years. At each
succeeding annual meeting of stockholders, directors shall be elected for a full
<PAGE>

term of three years to succeed the directors of the class whose terms expire at
such annual meeting.

                           Any vacancies on the Board of Directors resulting
from death, resignation, disqualification, removal, or other causes shall be
filled by either (i) the affirmative vote of the holders of a majority of the
voting power of the then-outstanding shares of voting stock of the corporation
entitled to vote generally in the election of directors (the "VOTING STOCK")
voting together as a single class; or (ii) by the affirmative vote of a majority
of the remaining directors then in office, even though less than a quorum of the
Board of Directors. Newly created directorships resulting from any increase in
the number of directors shall, unless the Board of Directors determines by
resolution that any such newly created directorship shall be filled by the
stockholders, be filled only by the affirmative vote of the directors then in
office, even though less than a quorum of the Board of Directors. Any director
elected in accordance with the preceding sentence shall hold office for the
remainder of the full term of the class of directors in which the new
directorship was created or the vacancy occurred and until such director's
successor shall have been elected and qualified.

                           In addition to the requirements of law and any other
provisions hereof (and notwithstanding the fact that approval by a lesser vote
may be permitted by law or any other provision hereof), the affirmative vote of
the holders of at least 66 2/3 percent of the voting power of the then
outstanding shares of stock of all classes and all series of the Corporation
entitled to vote generally in the election of directors, voting together as a
single class, shall be required to amend, alter, repeal, or adopt any provision
inconsistent with this Section (i) of this Article VI.

                  (ii) There shall be no right with respect to shares of stock
of the Corporation to cumulate votes in the election of directors.

                  (iii) Any director, or the entire Board of Directors, may be
removed from office at any time (i) with cause by the affirmative vote of the
holders of at least a majority of the voting power of the then-outstanding
shares of the Voting Stock, voting together as a single class; or (ii) without
cause by the affirmative vote of the holders of at least 66-2/3% of the voting
power of the then-outstanding shares of the Voting Stock.

                                   ARTICLE VII

         No action shall be taken by the stockholders of the Corporation other
than at an annual or special meeting of the stockholders, upon due notice and in
accordance with the provisions of the Corporation's bylaws.

                                  ARTICLE VIII

         The Corporation reserves the right to amend, alter, change or repeal
any provision contained in this Amended and Restated Certificate of
Incorporation, in the manner now or hereafter prescribed by statute, and all
<PAGE>

rights conferred upon stockholders herein are granted subject to this
reservation.

                                   ARTICLE IX

         The Board of Directors of the Corporation is expressly authorized to
make, alter or repeal Bylaws of the Corporation.

                                    ARTICLE X

         Meetings of stockholders may be held within or without the State of
Delaware, as the Bylaws may provide. The books of the Corporation may be kept
(subject to any provision contained in the statutes) outside the State of
Delaware at such place or places as may be designated from time to time by the
Board of Directors or in the Bylaws of the Corporation.

                                   ARTICLE XI

         The Corporation shall have perpetual existence.

                                   ARTICLE XII

         (A) To the fullest extent permitted by the General Corporation Law of
Delaware, as the same may be amended from time to time, a director of the
Corporation shall not be personally liable to the Corporation or its
stockholders for monetary damages for breach of fiduciary duty as a director. If
the General Corporation Law of Delaware is hereafter amended to authorize, with
the approval of a corporation's stockholders, further reductions in the
liability of the Corporation's directors for breach of fiduciary duty, then a
director of the Corporation shall not be liable for any such breach to the
fullest extent permitted by the General Corporation Law of Delaware, as so
amended.

         (B) Any repeal or modification of the foregoing provisions of this
Article XII shall not adversely affect any right or protection of a director of
the Corporation with respect to any acts or omissions of such director occurring
prior to such repeal or modification.

                                  ARTICLE XIII

         (A) To the fullest extent permitted by applicable law, the Corporation
is also authorized to provide indemnification of (and advancement of expenses
to) such agents (and any other persons to which Delaware law permits the
Corporation to provide indemnification) though bylaw provisions, agreements with
such agents or other persons, vote of stockholders or disinterested directors or
otherwise, in excess of the indemnification and advancement otherwise permitted
by Section 145 of the Delaware General Corporation Law, subject only to limits
created by applicable Delaware law (statutory or non-statutory), with respect to
actions for breach of duty to a corporation, its stockholders, and others.

<PAGE>

         (B) Any repeal or modification of any of the foregoing provisions of
this Article XIII shall not adversely affect any right or protection of a
director, officer, agent or other person existing at the time of, or increase
the liability of any director of the Corporation with respect to any acts or
omissions of such director, officer or agent occurring prior to such repeal or
modification."

                                      * * *

<PAGE>

         The foregoing Amended and Restated Certificate of Incorporation has
been duly adopted by this Corporation's Board of Directors and stockholders in
accordance with the applicable provisions of Section 228, 242 and 245 of the
General Corporation Law of the State of Delaware.

         Executed at San Mateo, California, on June 30, 1999.


                                               /s/ Christopher T. Keene
                                               ---------------------------------
                                               Christopher T. Keene
                                               Chief Executive Officer


                                               /s/ Christine Russell
                                               ---------------------------------
                                               Christine Russell
                                               Secretary