<PAGE>
 
                      SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, DC 20549

                                ---------------

                                 SCHEDULE 13G
                                (Rule 13d-102)



            INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT
          TO RULES 13d-1(b)(c), AND (d) AND AMENDMENTS THERETO FILED
                           PURSUANT TO RULE 13d-2(b)
                           (Amendment No. ______)/(1)/



                           MANHATTAN ASSOCIATES, INC.
                           --------------------------
                                 (Name of Issuer)

                     Common Stock, $.01 par value per share
                     --------------------------------------
                        (Title of Class of Securities)

                                  562750 10 9
                                  -----------
                                 (CUSIP Number)

                               December 31, 1998
                               -----------------
            (Date of Event Which Requires Filing of this Statement)


     Check the appropriate box to designate the rule pursuant to which this
Schedule is filed:

        [_]    Rule 13d-1(b)

        [_]    Rule 13d-1(c)

        [X]    Rule 13d-1(d)


___________
  /(1)/ The remainder of this cover page shall be filled out for a reporting
person's initial filing on this form with respect to the subject class of
securities, and for any subsequent amendment containing information which would
alter the disclosures provided in a prior cover page.

     The information required in the remainder of this cover page shall not be
deemed to be "filed" for purpose of Section 18 of the Securities Act of 1934 or
otherwise subject to the liabilities of that section of the Act but shall be
subject to all other provisions of the Act (however, see the Notes.)


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  CUSIP NO. 562750 10 9               13G                      Page 2 of 6 Pages
           -------------

 
- ------------------------------------------------------------------------------
      NAMES OF REPORTING PERSONS.
 1    I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY).
                                                                                
      Deepak Raghavan
                          
- ------------------------------------------------------------------------------
      CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS)
 2                                                              (a) [_]
                                                                (b) [_]
                                                 
- ------------------------------------------------------------------------------
      SEC USE ONLY
 3


- ------------------------------------------------------------------------------
      CITIZENSHIP OR PLACE OF ORGANIZATION
 4                                 
      India

- ------------------------------------------------------------------------------
                          SOLE VOTING POWER
                     5                                                       
     NUMBER OF            2,591,193/(1)/ 
                          
      SHARES       -----------------------------------------------------------
                          SHARED VOTING POWER
   BENEFICIALLY      6       
                          -0-
     OWNED BY
                   -----------------------------------------------------------
       EACH               SOLE DISPOSITIVE POWER
                     7       
    REPORTING             2,591,193/(1)/
 
      PERSON       -----------------------------------------------------------
                          SHARED DISPOSITIVE POWER
       WITH          8       
                          -0-
- ------------------------------------------------------------------------------
      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
 9                           
      2,591,193/(1)/

- ------------------------------------------------------------------------------
      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES
10    (SEE INSTRUCTIONS)
                                                                    [_]
 
- ------------------------------------------------------------------------------
      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9)
11           
      10.8%

- ------------------------------------------------------------------------------
      TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)
12           
      IN

- ------------------------------------------------------------------------------
___________
/(1)/ Includes 2,485,193 shares held by a limited partnership controlled by Mr.
Raghavan, the 99% limited partnership interest of which is owned by a trust for
the benefit of Mr. Raghavan's descendants, and 6,000 shares held by Mr. Raghavan
for the benefit of his minor child. Mr. Raghavan disclaims beneficial ownership
of the shares held by the limited partnership which are allocable to the
interest held by the trust and the shares held for the benefit of his minor 
child.


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CUSIP No. 562750 10 9                   13G                    Page 3 of 6 Pages
         --------------  

Item 1(a).  Name of Issuer:

                    Manhattan Associates, Inc.


Item 1(b).  Address of Issuer's Principal Executive Offices:

                    2300 Windy Ridge Parkway, Suite 700
                    Atlanta, GA  30339


Item 2(a).  Name of Person Filing:

                    Deepak Raghavan


Item 2(b).  Address of Principal Business Office or, if None, Residence:

                    2300 Windy Ridge Parkway, Suite 700
                    Atlanta, GA  30339

Item 2(c).  Citizenship:

                    India


Item 2(d).  Title of Class of Securities:

                    Common Stock, $.01 par value per share


Item 2(e).  CUSIP Number:

                    562750 10 9


Item 3.     If This Statement is Filed Pursuant to Rule 13d-1(b), or 13d-2(b) or
            (c), Check Whether the Person Filing is a:

       (a)   [_]   Broker or dealer registered under Section 15 of the 
                   Exchange Act.
                 
       (b)   [_]   Bank as defined in Section 3(a)(6) of the Exchange Act.
                 
       (c)   [_]   Insurance Company as defined in Section 3(a)(19) of the
                   Exchange Act.
                 
       (d)   [_]   Investment Company registered under Section 8 of the
                   Investment Company Act.
                 
       (e)   [_]   An investment adviser in accordance with Rule 
                   13d-1(b)(1)(ii)(E).
                 
       (f)   [_]   An employee benefit plan or endowment fund in 
                   accordance with Rule 13d-1(b)(1)(ii)(F).
                 
       (g)   [_]   A parent holding company or control person in 
                   accordance with Rule 13d-1(b)(1)(ii)(G).
                 
       (h)   [_]   A savings association as defined in Section 3(b) of         
                   the Federal Deposit Insurance Act.
                 
       (i)   [_]   A church plan that is excluded from the definition of an
                   investment company under Section 3(c)(14) of Investment
                   Company Act.


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CUSIP No. 562750 10 9                 13G                      Page 4 of 6 Pages
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      (j)    [_]   Group, in accordance with Rule 13d-1(b)(1)(ii)(J).

      If this statement is filed pursuant to Rule 13d-1(c), check this box. [_]


          Not applicable


Item 4.   Ownership.

          Provide the following information regarding the aggregate number and
percentage of the class of securities of the issuer defined in Item 1.

          (a)  Amount Beneficially Owned:  2,591,193/(1)/

          (b)  Percent of Class:  10.8%

          (c)  Number of shares as to which such person has:

               (i)    Sole power to vote or to direct the vote:  2,591,193/(1)/

               (ii)   Shared power to vote or to direct the vote:  -0-

               (iii)  Sole power to dispose or to direct the disposition of:

                      2,591,193/(1)/

               (iv)   Shared power to dispose or to direct the disposition of:  
                      -0-
            _________

            /(1)/  Includes 2,485,193 shares held by a limited partnership
            controlled by Mr. Raghavan, the 99% limited partnership interest of
            which is owned by a trust for the benefit of Mr. Raghavan's
            descendants, and 6,000 shares held by Mr. Raghavan for the benefit
            of his minor child. Mr. Raghavan disclaims beneficial ownership of
            the shares held by the limited partnership which are allocable to
            the interest held by the trust and the shares held for the benefit
            of his minor child.

     Instruction.  For computations regarding securities which represent a right
to acquire an underlying security, see Rule 13d-3(d)(1).


Item 5.   Ownership of Five Percent or Less of a Class.

          If this statement is being filed to report the fact that as of the
date hereof the reporting person has ceased to be the beneficial owner of more
than five percent of the class of securities, check the following [  ].

     Instruction.  Dissolution of a group requires a response to this item.

          Not Applicable.

Item 6.   Ownership of More than Five Percent on Behalf of Another Person.

          If any other person is known to have the right to receive or the power
to direct the receipt of dividends from, or the proceeds from the sale of, such
securities, a statement to that effect should be included in response to this
item and, if such interest relates to more than five percent of


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CUSIP No. 562750 10 9                 13G                      Page 5 of 6 Pages
         --------------          

the class, such person should be identified.  A listing of the shareholders of
an investment company registered under the Investment Company Act of 1940 or the
beneficiaries of an employee benefit plan, pension fund or endowment fund is not
required.

          Not applicable.


Item 7.   Identification and Classification of the Subsidiary Which Acquired the
          Security Being Reported on by the Parent Holding Company.

          If a parent holding company has filed this schedule, pursuant to Rule
13d-1(b)(ii)(G), so indicate under Item 3(g) and attach an exhibit stating the
identity and the Item 3 classification of the relevant subsidiary.  If a parent
holding company has filed this schedule pursuant to Rule 13d-1(c), attach an
exhibit stating the identification of the relevant subsidiary.

          Not applicable.


Item 8.   Identification and Classification of Members of the Group.

          If a group has filed this schedule, pursuant to Rule 13d-1(b)(ii)(J),
so indicate under Item 3(h) and attach an exhibit stating the identity and Item
3 classification of each member of the group.  If a group has filed this
schedule pursuant to Rule 13d-1(d), attach an exhibit stating the identification
of each member of the group.

          Not applicable.


Item 9.   Notice of Dissolution of Group.

          Notice of dissolution of a group may be furnished as an exhibit
stating the date of the dissolution and that all further filings with respect to
transactions in the security reported on will be filed, if required, by members
of the group, in their individual capacity.  See Item 5.

          Not applicable.


Item 10.  Certification.

          Not applicable.


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CUSIP No. 562750 10 9                 13G                      Page 6 of 6 Pages
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                                   SIGNATURE
                                        
          After reasonable inquiry and to the best of my knowledge and belief, I
certify that the information set forth in this statement is true, complete and
correct.

Date:  February 16, 1999

                                           By: /s/ Deepak Raghavan
                                               ---------------------------------
                                               Deepak Raghavan


          The original statement shall be signed by each person on whose behalf
the statement is filed or his authorized representative.  If the statement is
signed on behalf of a person by his authorized representative (other than an
executive officer or general partner of the filing person), evidence of the
representatives authority to sign on behalf of such person shall be filed with
the statement, provided, however, that a power of attorney for this purpose
which is already on file with the Commission may be incorporated by reference.
The name and title of each person who signs the statement shall be typed or
printed beneath his signature.

          Note.  Schedules filed in paper format shall include a signed original
and five copies of the schedule, including all exhibits.  See Rule 13d-7(b) for
other parties for whom copies are to be sent.

          Attention.  Intentional misstatements or omissions of fact constitute
federal criminal violations (see 18 U.S.C. 1001).