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.

(Continued on following pages)

(Page 1 of 5 Pages)

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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. 2 (“Amendment No. 2“) 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“), as amended by Amendment No. 1 filed with the SEC on May 30, 2017
(“Amendment No. 1” and together with the Original Schedule 13D and this Amendment No. 2, 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. 2 shall have the meanings set forth in the Schedule 13D. This Amendment No. 2 amends Items 2, 3, 5 and 7 as set forth below.
This is the final amendment to the Schedule 13D and constitutes an “exit filing” for the Reporting Person.

Item 2 of the Schedule 13D are hereby
amended and restated as follows:

(a) This statement is filed by JANA Partners
LLC, a Delaware limited liability company (the “Reporting Person“). The Reporting Person is a private money management
firm which holds Shares of the Issuer in various accounts under its management and control. The principal owner of the Reporting
Person is Barry Rosenstein (“Mr. Rosenstein” or the “Principal“).

(b) The principal business address of
the Reporting Person and the Principal is 767 Fifth Avenue, 8th Floor, New York, New York 10153.

(c) The principal business of the Reporting
Person and the Principal is investing for accounts under their management.

(d) Neither the Reporting Person nor
the Principal has, during the last five years, been convicted in a criminal proceeding (excluding traffic violations or similar
misdemeanors).

(e) Neither the Reporting Person nor
the Principal has, during the last five years, been a party to a civil proceeding of a judicial or administrative body of competent
jurisdiction and as a result of such proceeding was or is subject to a judgment, decree or final order enjoining future violations
of, or prohibiting or mandating activities subject to, federal or state securities laws or finding any violation with respect to
such laws.

(f) The Reporting Person is a limited
liability company organized in Delaware. The Principal is a citizen of the United States of America.

Item 3 of the Schedule 13D are hereby amended
and restated as follows:

As of the close of business on the date hereof,
the Reporting Person no longer may be deemed to beneficially own any Shares.

Item 5 of the Schedule 13D is hereby amended
and restated as follows:

(a) – (b) As of the close of business
on the date hereof, the Reporting Person no longer may be deemed to beneficially own any Shares.

The Reporting Person, Mr. Murphy, Ms.
Dietz, Mr. Dickson, Ms. Adler and Mr. Bittman are no longer deemed to be a “group” for purposes of Section 13(d)(3) of
the Exchange Act and Rule 13d-5(b)(1) promulgated thereunder. Therefore, the beneficial ownership reported in this Amendment No.
2 only includes the beneficial ownership of the Reporting Person.

(c) Information concerning transactions
in the Shares effected by the Reporting Person since the filing of Amendment No. 1 is set forth in Exhibit E hereto and
is incorporated herein by reference. All of the transactions in Shares listed hereto were effected in the open market through various
brokerage entities.

(d) No person (other than the Reporting
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, the Shares.

(e) July 18, 2017.

Item 7 of the Schedule 13D is being amended and supplemented by
the addition of the following:

Exhibit E: Transactions in the Shares effected since the
Filing of Amendment No. 1.

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: July 19, 2017