<PAGE>
                                                                    EXHIBIT 10.1

                              SECOND AMENDMENT TO
                     AMENDED AND RESTATED CREDIT AGREEMENT

     THIS SECOND AMENDMENT (this "Amendment") dated as of October 4, 1998 is
entered into by and among Einstein/Noah Bagel Corp., a Delaware corporation (the
"Borrower"), the lenders who are party to the Credit Agreement referred to below
(the "Lenders"), General Electric Capital Corporation, as Co-Agent (herein, in
such capacity, the "Co-Agent"), and Bank of America National Trust and Savings
Association, as Agent for the Lenders (herein, in such capacity, the "Agent").



                               W I T N E S E T H
                               - - - - - - - - -

     WHEREAS, the Borrower, the Lenders, the Co-Agent and the Agent are parties
to a certain Amended and Restated Secured Credit Agreement dated as of November
21, 1997 (as heretofore amended, called the "Credit Agreement"; terms used but
not otherwise defined herein are used herein as defined in the Credit
Agreement);

     WHEREAS, the Borrower desires to amend the Credit Agreement to revise the
Proforma System Fixed Charge Ratio covenant in certain respects; and

     WHEREAS, subject to the terms and conditions set forth herein the Agent,
the Co-Agent and the Lenders are willing to undertake such amendment;

     NOW, THEREFORE, in consideration of the premises, and intending to be
legally bound hereby, the Borrower, the Agent, the Co-Agent and the Lenders
hereby agree as follows:

     Section 1.  Amendment.

     Upon satisfaction of the conditions precedent set forth in Section 2 below
                                                                ---------      
and in reliance on the Borrower's warranties set forth in Section 3 below, as of
                                                          ---------             
the date hereof Section 7.5 of the Credit Agreement is amended to read in its
entirety as follows:
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     "SECTION 7.5.  Proforma System Fixed Charge Coverage Ratio. Maintain, as of
     the last day of each fiscal quarter occurring during the respective fiscal
     periods set forth below, a ratio of (1) Annualized System EBITDAL for such
     fiscal quarter to (2) Proforma Fixed Charges, as of such date, of not less
     than the ratio set forth below opposite such fiscal period; provided,
     however, for the purposes hereof, Proforma Fixed Charges shall exclude
     $12,000,000 of the final quarterly installment payment on the Term Loan due
     10/31/00:

                 Fiscal Period(s)         Covenant Level
                 ----------------         --------------
                 Q3/1998                  1.25:1.00
                 Q4/1998                  1.25:1.00
                 Q1 - Q2 1999             1.50:1.00
                 Q3 - Q4 1999             1.75:1.00
                 Q1 - Q4 2000             2.00:1.00

     Section 2.  Conditions Precedent.

     This Amendment shall become effective upon receipt by the Agent of (a) duly
executed counterpart signature pages from the Borrower and the Required Lenders,
and (b) payment in immediately available funds of an amendment fee of $30,000
paid by the Borrower to the Agent for the account of each Lender according to
its respective Percentage.

     Section 3.  Warranties.

     To induce the Agent, the Co-Agent and the Lenders to enter into this
Amendment, the Borrower warrants to the Agent, the Co-Agent and the Lenders as
of the date hereof that:

          (a)    The representations and warranties contained in the Credit
     Agreement and Loan Documents are true and correct in all material respects
     on and as of the date hereof (except to the extent such representations and
     warranties expressly refer to an earlier date); and

          (b)    No Default or Event of Default has occurred and is continuing.

                                      -2-
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     Section 4.  General.

          (a)    The Borrower agrees to pay on demand all reasonable costs and
     expenses in connection with the preparation, execution, and delivery of
     this Amendment, including, without limitation, the reasonable fees and out-
     of-pocket expenses of counsel for the Agent and the Co-Agent.

          (b)    As hereby modified, the Credit Agreement shall remain in full
     force and effect and is hereby ratified, approved and confirmed in all
     respects.

          (c)    This Amendment shall be binding upon and shall inure to the
     benefit of the Borrower, the Lenders, the Co-Agent and the Agent and
     respective successors and assigns of the Lenders, the Co-Agent and the
     Agent.

          (d)    This Amendment may be executed in any number of counterparts
     and by the different parties on separate counterparts, and each such
     counterpart shall be deemed to be an original, but all such counterparts
     shall together constitute but one and the same Amendment.


                                   * * * * *

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Delivered at Chicago, Illinois, as of the date and year first above written.

                              EINSTEIN/NOAH BAGEL CORP.

                              By:  /s/ Paul A. Strasen
                                  --------------------------------
                              Title:   Senior Vice President
                                     -----------------------------
 

                              BANK OF AMERICA NATIONAL TRUST AND
                              SAVINGS ASSOCIATION, as Agent

                              By:  /s/ David A. Johanson
                                  --------------------------------
                              Title:   Vice President
                                     -----------------------------


                              BANK OF AMERICA NATIONAL TRUST AND 
                              SAVINGS ASSOCIATION, as Lender

                              By:  /s/ Marcia Clausen
                                  --------------------------------
                              Title:   Managing Partner
                                     -----------------------------


                              GENERAL ELECTRIC CAPITAL 
                              CORPORATION, as Co-Agent and Lender

                              By:  /s/ Fred Maurice
                                  --------------------------------
                              Title:   Vice President-Risk Manager
                                     -----------------------------


                              LASALLE NATIONAL BANK

                              By:  /s/ John C. Thurston
                                  --------------------------------
                              Title:   Assistant Vice President
                                     -----------------------------

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     The undersigned hereby acknowledge the foregoing amendments and reaffirm 
their respective duties and obligations arising under the Loan Documents to 
which each is a party.

                                             EINSTEIN NOAH BAGEL PARTNERS, INC.

                                            
                                             By: /s/ Paul A. Strasen
                                                -------------------------------
                                             Title:  Vice President
                                                    ---------------------------

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