<PAGE>

                                                                   Exhibit 10.16


                     NINTH AMENDMENT TO AMENDED AND RESTATED
                        AGREEMENT OF LIMITED PARTNERSHIP
                                       OF
                     BRANDYWINE OPERATING PARTNERSHIP, L.P.

         THIS NINTH AMENDMENT, dated as of May 7, 1999 (the "Amendment"),
further amends the Amended and Restated Agreement of Limited Partnership
Agreement (as amended to date, the "Partnership Agreement") of BRANDYWINE
OPERATING PARTNERSHIP, L.P., a Delaware limited partnership (the "Partnership").
Capitalized terms used herein but not defined herein shall have the meanings
given such terms in the Partnership Agreement.

                                   BACKGROUND
                                   ----------

     C. Pursuant to the Partnership Agreement, Brandywine Realty Trust (the
"General Partner"), as the general partner of the Partnership, has the power and
authority to issue additional Partnership Interests to persons on such terms and
conditions as the General Partner may deem appropriate.

     D. The General Partner, pursuant to the exercise of such power and
authority and in accordance with the Partnership Agreement, has determined to
execute this Amendment to the Partnership Agreement to evidence the issuance of
additional Partnership Interests and the admission of the other signatories
hereto as Limited Partners of the Partnership in exchange for certain
contributions of interests in real estate and real estate related assets that
are being made to the Partnership on the date hereof pursuant to a
"contribution" agreement (relating to properties owned by persons and entities
that include Donald E. Axinn and affiliates) among the Partnership and the other
signatories thereto.

         NOW, THEREFORE, in consideration of the mutual covenants and agreements
herein contained and other good and valuable consideration, the receipt,
adequacy and sufficiency of which are hereby acknowledged, the parties hereto,
intending to be legally bound, hereby amend the Partnership Agreement as
follows:

         1. The Partnership Agreement is hereby amended to reflect the admission
as a Limited Partner on the date hereof of the Persons set forth on Schedule A
attached hereto (the "Admitted Partners") and the ownership by such Persons of
the number of Class A Units listed opposite each Person's name on Schedule A.
Attached as Schedule B is a list of the Partners of the Partnership prior to the
admission of the Admitted Partners, together with the number and class of
Partnership Interests owned by such partners.

         2. The Partnership Interests issued hereby shall constitute Class A
Units; provided that any distribution to be received by the Admitted Partners on
the Class A Units issued to them on the date hereof on account of the fiscal
quarter in which they are admitted to the Partnership shall be pro-rated to
reflect the portion of the fiscal quarter of the Partnership for which the
Admitted Partners held such Class A Units and shall not be pro-rata in


<PAGE>


accordance with their then Percentage Interests; provided further that the
Redemption Right granted to holders of Class A Units in Article XV of the
Partnership Agreement shall not be exercisable by the holders of the Class A
Units issued on the date hereof to the Admitted Partners until the first
anniversary of the date hereof, except that (i) if the holder of any such Class
A Units dies, such holder's estate shall thereupon be permitted to exercise the
Redemption Right with respect to all of such Class A Units held by it
notwithstanding the foregoing restriction and (ii) if a Change of Control (as
defined below) of the General Partner occurs, the foregoing restriction on
exercise of the Redemption Right shall automatically terminate with respect to
all of such Class A Units. Notwithstanding anything contained in the Partnership
Agreement or this Amendment, if the holder of Class A Units exercises its
Redemption Right and the General Partner or the holder reasonably believes that
the issuance of Common Shares in satisfaction of the Redemption Right would
require a notification and filing under the Hart-Scott-Rodino Antitrust
Improvements Act of 1976, as amended (the "HSR Act"), the obligation of the
Partnership and the General Partner to satisfy the Redemption Right may be
suspended until applicable filings with the Federal Trade Commission and the
Antitrust Division of the Department of Justice have been made and the
applicable waiting periods have expired. The General Partner agrees to use
commercially reasonable efforts to make any requisite filings under the HSR Act
in order to promptly obtain expiration of the applicable waiting periods, and
the Partnership and the applicable holder of Class A Units shall split equally
any filing fees that may be payable under the HSR Act.

         3. As used herein, the term "Change of Control" shall mean Change of
Control" means:

                  (i)      the acquisition in one or more transactions by any
                           "Person" (as the term person is used for purposes of
                           Sections 13(d) or 14(d) of the Exchange Act) of
                           "Beneficial ownership" (within the meaning of Rule
                           13d-3 promulgated under the Exchange Act) of
                           twenty-five percent (25%) or more of the combined
                           voting power of the General Partner's then
                           outstanding voting securities (the "Voting
                           Securities"), provided that for purposes of this
                           clause (i) Voting Securities acquired directly from
                           the General Partner by any Person shall be excluded
                           from the determination of such Person's Beneficial
                           ownership of Voting Securities (but such Voting
                           Securities shall be included in the calculation of
                           the total number of Voting Securities then
                           outstanding); or

                  (ii)     approval by shareholders of the General Partner of:

                           (A)  a merger, reorganization or consolidation
                                involving the General Partner if the
                                shareholders of the General Partner immediately
                                before such merger, reorganization or
                                consolidation do not or will not own directly or
                                indirectly immediately following such merger,
                                reorganization or consolidation, more than fifty
                                percent (50%) of the combined voting power of
                                the outstanding voting securities of the General
                                Partner resulting from or surviving such merger,
                                reorganization or consolidation in substantially
                                the same proportion as their ownership of the
                                Voting Securities outstanding immediately before
                                such merger, reorganization or consolidation; or

<PAGE>


                           (B)  a complete liquidation or dissolution of the
                                General Partner; or

                           (C)  an agreement for the sale or other disposition
                                of all or substantially all of the assets of the
                                General Partner; or

                  (iii)    acceptance by shareholders of the General Partner of
                           shares in a share exchange if the shareholders of the
                           General Partner immediately before such share
                           exchange do not or will not own directly or
                           indirectly immediately following such share exchange
                           more than fifty percent (50%) of the combined voting
                           power of the outstanding voting securities of the
                           entity resulting from or surviving such share
                           exchange in substantially the same proportion as
                           their ownership of the Voting Securities outstanding
                           immediately before such share exchange.

         4. By execution of this Amendment to the Partnership Agreement by the
General Partner, the Admitted Partners agree to be bound by each and every term
of the Partnership Agreement as amended from time to time in accordance with the
terms of the Partnership Agreement. The General Partner confirms that the
provisions in Section 18.1(a) of the Partnership Agreement shall apply to the
Admitted Partners notwithstanding Section 18.7 of the Partnership Agreement.

         5. On the date of this Amendment, each of the Admitted Partners shall
execute and deliver to Brandywine Realty Trust an Irrevocable Proxy coupled with
an Interest in the form set forth on Exhibit 1 hereto attached.

         6. Except as expressly set forth in this Amendment to the Partnership
Agreement, the Partnership Agreement is hereby ratified and confirmed in each
and every respect.



<PAGE>


         IN WITNESS WHEREOF, this Amendment to the Partnership Agreement has
been executed and delivered as of the date first above written.

                                     GENERAL PARTNER:
                                     ---------------

                                     BRANDYWINE REALTY TRUST

                                     By:
                                        ---------------------------------------
                                          Gerard H. Sweeney
                                          President and Chief Executive Officer

                                     ADMITTED PARTNERS:
                                     -----------------


                                     ------------------------------------------
                                     Donald E. Axinn, individually


<PAGE>


                                  SCHEDULE "A"


                                                               NUMBER OF
          ADMITTED                                            PARTNERSHIP
          PARTNERS                                             INTERESTS
          --------                                            -----------
Donald E. Axinn



<PAGE>
                                  SCHEDULE "B"

                     BRANDYWINE OPERATING PARTNERSHIP, L.P.
                        OUTSTANDING PARTNERSHIP INTERESTS
                                AS OF MAY 7, 1999
<TABLE>
<CAPTION>
                                                                  NUMBER OF PARTNERSHIP INTERESTS
                                                                  (ALL CLASS A UNITS,
LIMITED PARTNERS                                                  UNLESS OTHERWISE INDICATED)
----------------                                                  ---------------------------
<S>                                                                          <C>
The Nichols Company                                                          2,742
Brian F. Belcher                                                             7,245
Jack R. Loew                                                                 1,245
Craig C. Hough                                                               1,245
Werner A. Fricker                                                            6,830
Randle Scarborough                                                           59,578
Sean Scarborough                                                             60,576
Steven L. Shapiro                                                            1,902
Robert K. Scarborough                                                        215,384
Raymond J. Perkins                                                           2,536
Brandywine Holdings I, Inc.                                                  5
Brandywine Realty Trust                                                      467,220
Brookstone Investors, L.L.C.                                                 57,126
Brookstone Holdings of Del.-4, L.L.C.                                        7,579
Brookstone Holdings of Del.-5, L.L.C.                                        80,445
Brookstone Holdings of Del.-6, L.L.C.                                        7,886
John S. Trogner, Sr.                                                         89,801.232
John S. Trogner, Jr.                                                         73,048.310
Blair S. Trogner, Sr.                                                        138,126.471
Emma B. Trogner                                                              27,087.416
Ronalee Trogner                                                              21,669.933
Candis C. Trogner                                                            40,631.123
Arthur and Marion Eberstein                                                  7,513
Calvin Axinn                                                                 40,927
Estate Irving Hirshman                                                       1,488
Trust UTW of Theodore Geffner                                                485
Gloria Kantor                                                                21,647
Helen Geffner                                                                1,488
Howard Kantor                                                                31,505
Leo Guthart                                                                  876
Morris Green                                                                 50,233
Richard Bernhard                                                             40,927
Lennard Axinn                                                                2,156
Donald E. Axinn                                                              928,651
William H. Goodwin, Jr.                                                      41,734
Bryson Powell                                                                41,734
Brandywine Realty Trust                                                      750,000 Series A Preferred Mirror
                                                                                     Units

</TABLE>

<PAGE>

<TABLE>
<CAPTION>
                                                                  NUMBER OF PARTNERSHIP INTERESTS
                                                                  (ALL CLASS A UNITS,
LIMITED PARTNERS                                                  UNLESS OTHERWISE INDICATED)
----------------                                                  ---------------------------
<S>                                                                          <C>
Commonwealth Atlantic Operating Properties Inc.                             1,140,527 Series B Preferred
                                                                                      Units
Commonwealth Atlantic Land II Inc.                                          283,731   Series B Preferred Units
Commonwealth Atlantic Development Inc.                                      43,725    Series B Preferred Units
Commonwealth Atlantic Land Company                                          82,017    Series B Preferred Units
Brandywine Realty Trust                                                     1,041,667 Series C Preferred
                                                                                      Mirror Units
</TABLE>

<TABLE>
<CAPTION>
GENERAL PARTNER                                                   NUMBER OF PARTNERSHIP INTERESTS
---------------                                                   -------------------------------
<S>                                                                         <C>
Brandywine Realty Trust                                                     37,544,430 GP Units

</TABLE>


<PAGE>
                                   EXHIBIT "1"

                   IRREVOCABLE PROXY COUPLED WITH AN INTEREST


                  KNOWN ALL MEN BY THESE PRESENTS, that the undersigned hereby
irrevocably constitutes and appoints the General Partner, any Liquidating
Trustee, and authorized officers and attorneys-in-fact of each, and each of
those acting singly, in each case with full power of substitution, as its true
and lawful agent and attorney-in-fact, with full power and authority in its
name, place and stead to: execute, swear to, acknowledge, deliver, file and
record in the appropriate public offices (i) all certificates, documents and
other instruments (including, without limitation, this Agreement and the
Certificate and all amendments or restatements thereof) that the General Partner
or the Liquidating Trustee deems appropriate or necessary to form, qualify or
continue the existence or qualification of the Partnership as a limited
partnership (or a partnership in which the limited partners have limited
liability) in the State of Delaware and in all other jurisdictions in which the
Partnership may conduct business or own property; (ii) all instruments that the
General Partner deems appropriate or necessary to reflect any amendment, change,
modification or restatement of this Agreement in accordance with the terms of
this Agreement; (iii) all conveyances and other instruments or documents that
the General Partner deems appropriate or necessary to reflect the dissolution
and liquidation of the Partnership pursuant to the terms of this Agreement,
including, without limitation, a certificate of cancellation; and (iv) all
instruments relating to the admission, withdrawal, removal or substitution of
any Partner pursuant to the provisions of this Agreement, or the Capital
Contribution of any Partner. The foregoing power of attorney is irrevocable and
a power coupled with an interest, in recognition of the fact that each of the
Partners will be relying upon the power of the General Partner to act as
contemplated by this Agreement in any filing or other action by it on behalf of
the Partnership, and it shall survive the death, incapacity or incompetency of a
Limited Partner to the effect and extent permitted by law and the Transfer of
all or any portion of such Limited Partner's Partnership Units and shall extend
to such Limited Partner's heirs, distributees, successors, assigns and personal
representatives.

                  IN WITNESS WHEREOF, the undersigned has executed and delivered
this Proxy on this 7th day of May, 1999.

                                           ---------------------------------
                                           Donald E. Axinn, individually