13D Filing: JANA Partners and Whole Foods Market Inc (WFM)

If the filing person has previously filed a statement on Schedule
13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of Rule 13d-1(e), 13d-1(f)
or 13d-1(g), check the following box. [ ]

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

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The information required on the remainder of this cover page shall
not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (“Act”) 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).

This Amendment No. 1 (“Amendment No. 1“) amends
and supplements the statement on Schedule 13D filed with the Securities and Exchange Commission (the “SEC“) on
April 10, 2017 (the “Original Schedule 13D“, and together with this Amendment No. 1, the “Schedule 13D“)
with respect to the shares (“Shares“) of common stock, no par value, of Whole Foods Market, Inc., a Texas corporation
(the “Issuer“). Capitalized terms used herein and not otherwise defined in this Amendment No. 1 shall have the
meanings set forth in the Original Schedule 13D. This Amendment No. 1 amends Items 3, 4, 5(a), 5(b), 5(c) and 6.

The first two sentences of Item 3 of the Schedule
13D are hereby amended and restated as follows:

The 27,642,498 Shares reported herein as beneficially
owned by the Reporting Persons were acquired at an aggregate purchase price of approximately $841.8 million.

The 26,074,830 Shares reported herein by JANA
were acquired at an aggregate purchase price of approximately $794.5 million.

Item 4 of the Schedule 13D is hereby amended
and supplemented by the addition of the following:

On May 27, 2017, JANA entered into a nominee
agreement with Celeste A. Clark, Ph.D. (“Dr. Clark“) substantially in the form attached as Exhibit B to the Schedule
13D filed by JANA with the Securities and Exchange Commission on April 10, 2017 and incorporated by reference herein.

The principal business of Dr. Clark is consulting on nutrition, health policy, regulatory matters and leadership
after previously serving as Senior Vice President of Global Public Policy and External Affairs and Chief Sustainability Officer
of Kellogg Company.  Dr. Clark currently serves on the boards of Mead Johnson Nutrition Company and AdvancePierre Foods.

Paragraphs (a) and (b) of Item 5 of the Schedule
13D are hereby amended and restated and paragraph (c) of Item 5 of the Schedule 13D is hereby amended and supplemented as follows:

(a) The aggregate percentage of Shares
reported to be beneficially owned by the Reporting Persons is based upon 319,564,636 Shares outstanding, which is the total number
of Shares outstanding as of May 12, 2017, as reported in the Issuer’s Quarterly Report on Form 10-Q for the quarterly period ended
April 9, 2017, filed with the SEC on May 19, 2017.

As of the close of business on the date
hereof, JANA may be deemed to beneficially own 26,074,830 Shares, representing approximately 8.2% of the Shares outstanding.

As of the close of business on the date
hereof, Mr. Murphy may be deemed to beneficially own 1,457,078 Shares, representing approximately 0.5% of the Shares outstanding.

As of the close of business on the date
hereof, Ms. Dietz may be deemed to beneficially own 101,000 Shares, representing less than 0.1% of the Shares outstanding.

As of the close of business on the date
hereof, Mr. Dickson may be deemed to beneficially own 5,275 Shares, representing less than 0.1% of the Shares outstanding.

As of the close of business on the date
hereof, Ms. Adler may be deemed to beneficially own 3,455 Shares, representing less than 0.1% of the Shares outstanding.

As of the close of business on the date
hereof, Mr. Bittman may be deemed to beneficially own 860 Shares, representing less than 0.1% of the Shares outstanding.

By virtue of the Nominee Agreements (as
defined in Item 6) and the Consulting Agreements (as defined in Item 6), JANA, each of the Potential Nominees (as defined in Item
6) who may deemed to beneficially own Shares as described in Item 5(a) of the Schedule 13D and each of the Consultants (as defined
in Item 6) may be deemed to have formed a “group” within the meaning of Section 13(d)(3) of the Exchange Act and may
be deemed to beneficially own an aggregate of 27,642,498 Shares, representing approximately 8.7% of the outstanding Shares. Each
Potential Nominee expressly disclaims beneficial ownership of the Shares beneficially owned by JANA, each other Potential Nominee
and each Consultant. JANA expressly disclaims beneficial ownership of the Shares beneficially owned by each Potential Nominee and
each Consultant. Each Consultant expressly disclaims beneficial ownership of the Shares beneficially owned by JANA, each other
Consultant and each Potential Nominee.

(b) JANA has sole voting and dispositive
power over 26,074,830 Shares, which power is exercised by the Principal. Mr. Murphy has sole voting and dispositive power over
the 1,457,078 Shares beneficially owned by him. Ms. Dietz has sole voting and dispositive power over the 101,000 Shares beneficially
owned by her. Mr. Dickson has sole voting and dispositive power over the 5,275 Shares beneficially owned by him. Ms. Adler has
sole voting and dispositive power over the 3,455 Shares beneficially owned by her. Mr. Bittman has sole voting and dispositive
power over the 860 Shares beneficially owned by him.

(c) The previously reported
options held by the Reporting Persons were automatically exercised in-the-money according to their terms on their maturity
date of May 19, 2017, for an exercise price of $27.00 for options to purchase 2,810,000 Shares and for an exercise price of
$28.00 for options to purchase 725,000 Shares. As of the date hereof, the Reporting Persons no longer have trading authority
over 239,537 of the Shares previously reported. Except as set forth herein, the Reporting Persons did not affect any
transactions in the Shares since the filing of Original Schedule 13D.

The first sentence of Item 6 of the Schedule
13D is hereby amended and restated as follows:

Each of Mr. Murphy, Mr. Dickson, Ms. Adler,
and Dr. Clark (each, the “Potential Nominee“) have entered into a nominee agreement (the “Nominee Agreement“)
with JANA substantially in the form attached as Exhibit B to the Schedule 13D whereby each Potential Nominee agreed to become
a member of a slate of nominees (the “Slate“) and stand for election as a director of the Issuer in connection
with a proxy solicitation (the “Proxy Solicitation“) which may be conducted by JANA in respect of the 2018 annual
meeting of stockholders of the Issuer (the “2018 Annual Meeting“).

The third paragraph of Item 6 of the Schedule
13D is hereby amended and supplemented as follows:

As of May 19, 2017, JANA is no longer party
to any call options.

SIGNATURES

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.

Dated: May 30, 2017