13D Filing: Jab Forest B.v. and Panera Bread Co (NASDAQ:PNRA)

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

SCHEDULE 13D

INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO § 240.13d-1(a)

AND AMENDMENTS THERETO FILED PURSUANT TO § 240.13d-2(a)

Panera Bread Company

(Name of Issuer)

Class
A Common Stock, Par Value $0.0001 Per Share

Class B Common Stock, Par Value $0.0001 Per Share

(Title of Class of Securities)

69840W108 / 69840W207

(CUSIP Number)

Joachim
Creus

Rye Parent Corp.

c/o JAB Holding Company LLC

1701 Pennsylvania Avenue NW, Suite 801

Washington, DC 20006

Tel.: (202) 602-1301

(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

Copies to:

Paul T. Schnell, Esq.

Sean C. Doyle, Esq.

Maxim O. Mayer-Cesiano, Esq.

Skadden, Arps, Slate, Meagher & Flom LLP

Four Times Square

New
York, New York 10036

Tel.: (212) 735-3000

April 4, 2017

(Date of
Event Which Requires Filing of This Statement)

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.  ☐

Item 1. Security and Issuer.

This statement on Schedule 13D (this Statement) relates to the Class A Common Stock, par value $0.0001 per share (the
Class A Common Stock), and the Class B Common Stock, par value $0.0001 per share (the Class B Common Stock) (the shares of Class A Common Stock and the shares of Class B Common Stock, each a
Share and, collectively, the Shares) of Panera Bread Company, a Delaware corporation (PNRA), and is being filed pursuant to Section 13(d) of the Securities Exchange Act of 1934 (the Exchange Act).
PNRAs principal executive offices are located at 3630 South Geyer Road, Suite 100, St. Louis, Missouri 63127.

Item 2. Identity and
Background.

(a)-(c) This Statement is being filed jointly on behalf of (i) Rye Parent Corp., a Delaware corporation (Rye
Parent), (ii) Rye Merger Sub, Inc., a Delaware corporation, a direct wholly owned subsidiary of Rye Parent (Merger Sub), (iii) Rye Parent Holdings Corp., a Delaware corporation, which is the parent company of Rye Parent (Rye
Parent Holdco), (iv) Rye Holdings I Inc., a Delaware corporation, which is the parent company of Rye Parent Holdco (Rye Holdings), (v) JAB Forest B.V., a private limited liability company incorporated under the laws of the
Netherlands, which is the parent company of Rye Holdings (Forest), (vi) JAB Holdings B.V., a private limited liability company incorporated under the laws of the Netherlands, which is the parent company of Forest (JAB
Holdings), (vii) JAB Investments S.à r.l., a private limited liability company incorporated under the laws of Luxembourg, which is the parent company of JAB Holdings (JAB Investments), (viii) JAB Holding Company S.à
r.l., a private limited liability company incorporated under the laws of Luxembourg, which is the parent company of JAB Investments (JAB Holding Company), (ix) Donata Holdings B.V., a private limited liability company incorporated under
the laws of the Netherlands, which is a parent company of JAB Holding Company (Donata), (x) Agnaten SE, a private company incorporated under the laws of Austria, which is a parent company of JAB Holding Company (Agnaten), and
(xi) Lucresca SE, a private company incorporated under the laws of Austria, which is the parent company of Donata (Lucresca, and together with Rye Parent, Merger Sub, Rye Parent Holdco, Rye Holdings, Forest, JAB Holdings, JAB
Investments JAB Holding Company, Donata, and Agnaten, the Reporting Persons).

Each of Parents, Merger Subs, Rye
Parent Holdcos, and Rye Holdings executive office is located at c/o JAB Holding Company LLC, 1701 Pennsylvania Avenue NW, Suite 801, Washington, DC 20006, and the telephone number of each is (202)
602-1301. The principal business address of each of Forest, JAB Holdings, JAB Investments, JAB Holding Company and Donata is Oosterdoksstraat 80, 1011 DK Amsterdam, The Netherlands. The principal business
address of Agnaten and Lucresca is Rooseveltplatz 45 / Top 10, A1090 Vienna, Austria.

JAB Holding Company and its affiliated
group of companies, of which Rye Parent, Merger Sub, Rye Parent Holdco, and Rye Holdings are members, is a Luxembourg based and privately held group focused on long-term investments in companies with premium brands in the consumer goods category.
Merger Sub is a direct wholly owned subsidiary of Rye Parent, and was recently incorporated for the purpose of acquiring all of the issued and outstanding Shares and consummating the transactions contemplated by the Merger Agreement (as defined
below) and, to date, has engaged and is expected to engage in no other activities other than those incidental to the Merger (as defined below) and the Merger Agreement. Until immediately prior to the time Merger Sub purchases the Shares, it is not
anticipated that Merger Sub will have any significant assets or liabilities.

The name, business address and present principal occupation
or employment of each executive officer and director of Rye Parent, Merger Sub, Rye Parent Holdco, Rye Holdings, Forest, JAB Holdings, JAB Investments, JAB Holding Company, Donata, Agnaten and Lucresca are set forth on Schedule A hereto and
incorporated herein by reference.

(d) During the last five years, none of the Reporting Persons, and to the best knowledge of each of the
Reporting Persons, none of the persons named on Schedule A has been convicted in a criminal proceeding (excluding traffic violations or similar misdemeanors).

(e) During the last five years, none of the Reporting Persons, and to the best knowledge of each of the Reporting Persons, none of the persons
named on Schedule A was 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 citizenship of each executive officer
and director of the Reporting Persons is set forth on Schedule A.

The Reporting Persons have entered into a Joint Filing Agreement, dated
as of April 13, 2017, a copy of which is attached as Exhibit 1 hereto, pursuant to which the Reporting Persons have agreed to file this statement jointly in accordance with the provisions of Rule
13d-1(k)(1) of the Exchange Act.

Item 3. Source and Amount of Funds or Other Consideration.

Pursuant to, and subject to the terms and conditions contained in, the Voting Agreement (as defined below) described in Item 4 of this
Statement, the Reporting Persons may be deemed to have acquired beneficial ownership of the Subject Shares (as defined below) by virtue of the execution of the Voting Agreement by Rye Parent, Merger Sub and certain stockholders of PNRA. As a result
of Merger Sub being its indirect wholly owned subsidiary, Rye Parent Holdco, Rye Holdings, Forest, JAB Holdings, JAB Investments, JAB Holding Company, Donata, Agnaten, and Lucresca may be deemed to share beneficial ownership of the Subject Shares
that Merger Sub may be deemed to beneficially own. No payments were made by or on behalf of the Reporting Persons in connection with the execution of the Merger Agreement or the execution of the Voting Agreement. It is currently anticipated that Rye
Parent or Merger Sub will finance the acquisition of Shares in the Merger through a combination of the issuance of debt by affiliates of Bank of America, N.A., JPMorgan Chase Bank, N.A., and Goldman Sachs Bank USA, as well as equity contributions by
the Reporting Persons, affiliates of BDT Capital Partners, LLC, and potentially other parties.

Item 4. Purpose of
Transaction.

Merger Agreement

On April 4, 2017, Rye Parent, Merger Sub, and JAB Holdings entered into an Agreement and Plan of Merger (the Merger Agreement)
with PNRA, providing for the merger of Merger Sub with and into PNRA (the Merger), with PNRA surviving the Merger as a wholly owned subsidiary of Rye Parent. Subject to the terms and conditions of the Merger Agreement, at the effective
time of the Merger (the Effective Time), each issued and outstanding Share, except for certain excluded shares, will be automatically cancelled and converted into the right to receive $315.00 in cash (the Merger
Consideration).

In addition, subject to the terms and conditions of the Merger Agreement, at the Effective Time, (a) each
outstanding stock option and stock appreciation right of PNRA will accelerate and will be converted into the right to receive a cash amount based on the spread, if any, between the Merger Consideration and the exercise price payable per share under
such stock option or stock appreciation right, as applicable, (b) each outstanding restricted share of PNRA will accelerate and receive the same treatment as the Common Stock, in each case, paid as soon as reasonably practicable after the
Effective Time, net of any applicable withholding taxes. In addition, each outstanding performance award of PNRA will be cancelled and converted into the right to receive a cash amount based on the greater of target and actual performance determined
through the Effective Time, to be paid as follows: (i) a pro-rata portion of each performance award will be paid as soon as reasonably practicable after the Effective Time; and (ii) the remaining
portion of each performance award will be paid on the earlier of the date on which such performance award was originally scheduled to vest (subject to the holders continued employment with PNRA or any of its affiliates through such date), and
the holders termination of employment without cause or resignation for good reason, in each case, net of any applicable withholding taxes.

Consummation of the Merger is subject to the satisfaction or waiver of specified closing conditions, including (i) the adoption of the
Merger Agreement by the affirmative vote of the holders of a majority of the voting power of the shares of Common Stock issued and outstanding and entitled to vote at a meeting of PNRAs stockholders, (ii) the expiration or termination of
the applicable waiting period under the Hart-Scott-Rodino Antitrust Improvements Act of 1976, and (iii) other customary closing conditions, including (a) the absence of any law, order, or pending action by a

governmental entity prohibiting or seeking to prohibit the Merger or the other transactions contemplated by the Merger Agreement, (b) the accuracy of each partys representations and
warranties (subject to customary materiality qualifiers), (c) each partys performance of its obligations and covenants contained in the Merger Agreement and (d) as a condition to Rye Parents obligation to close the merger, the
absence of any Material Adverse Effect (as defined in the Merger Agreement) on PNRA.

The Merger Agreement also contains customary
representations, warranties and covenants of PNRA, JAB Holdings, Rye Parent, and Merger Sub. PNRA has also made certain covenants in the Merger Agreement, including covenants regarding the operation of the business of PNRA and its subsidiaries prior
to the Effective Time of the Merger. PNRA has also agreed to a customary non-solicitation covenant in the Merger Agreement prohibiting PNRA from (a) soliciting, providing
non-public information or engaging or participating in any discussions or negotiations concerning proposals relating to alternative business combination transactions, or (b) entering into an acquisition
agreement in connection with such an alternative business combination transaction, in each case, except as permitted under the Merger Agreement (including a customary exception for PNRAs board of directors to consider certain unsolicited
proposals relating to alternative business combination transactions received prior to the adoption of the Merger Agreement by PNRAs stockholders, but subject to Rye Parents right to match, or otherwise propose amendments to its
transaction in response to, any such acquisition proposal during a specified notice period).

The Merger Agreement may be terminated by
each of PNRA and Rye Parent under certain circumstances, including if the Merger is not consummated by October 4, 2017 (provided that no party may terminate the Merger Agreement if such partys breach primarily contributed to the failure
of a condition to consummate the Merger by such date). The Merger Agreement also provides for certain other customary termination rights for PNRA and Rye Parent, and further provides that a termination fee in the amount of $215 million will be
payable by PNRA to Rye Parent in connection with the termination of the Merger Agreement under certain specified circumstances, including if PNRA terminates the Merger Agreement in order to accept a superior proposal for an alternative business
combination transaction and enters into an acquisition agreement related to such superior proposal.

The representations, warranties and
covenants of each of PNRA, JAB Holdings, Rye Parent, and Merger Sub contained in the Merger Agreement have been made solely for the benefit of the parties to the Merger Agreement. In addition, such representations, warranties and covenants
(i) have been made only for purposes of the Merger Agreement, (ii) have been qualified by confidential disclosures made by the parties in connection with the Merger Agreement, (iii) are subject to materiality qualifications contained
in the Merger Agreement which may differ from what may be viewed as material by investors, (iv) were made only as of the date of the Merger Agreement or such other date as is specified in the Merger Agreement and (v) have been included in
the Merger Agreement for the purpose of allocating risk between the contracting parties rather than establishing matters as facts. The Merger Agreement has been included only to provide investors with information regarding the terms of the Merger
Agreement, and not to provide investors with any other factual information regarding the parties or their respective businesses. Investors should not rely on the representations, warranties and covenants or any descriptions thereof as
characterizations of the actual state of facts or condition of the parties or any of its subsidiaries or affiliates. Moreover, information concerning the subject matter of the representations and warranties may change after the date of the Merger
Agreement, which subsequent information may or may not be fully reflected in the public disclosures by the parties or their subsidiaries. The Merger Agreement should not be read alone, but should instead be read in conjunction with the other
information regarding the parties that is or will be contained in, or incorporated by reference into, the Forms 10-K, Forms 10-Q and other documents that the
parties file with the Securities and Exchange Commission.

Voting Agreement

On April 4, 2017, Ronald M. Shaich, PNRAs Founder, Chairman and Chief Executive Officer, and certain stockholders of PNRA affiliated
with Mr. Shaich (including entities for which Domenic Colasacco, a director of PNRA, serves as a trustee or manager) (collectively with Mr. Shaich, the Shaich Holders), entered into a voting agreement with Rye Parent and Merger
Sub (the Voting Agreement) pursuant to which the Shaich Holders have agreed to, among other things, vote in favor of the adoption of the Merger Agreement and the transactions contemplated by the Merger Agreement at any meeting of the
stockholders of PNRA prior to the termination of the Voting Agreement, subject to

certain exceptions (including the permitted transfer of the Shares). The Shaich Holders have the power to vote in the aggregate approximately 15.5% of the voting power of the Shares issued and
outstanding, represented by 49,759 shares of Class A Common Stock, 1,311,690 shares of Class B Common Stock, and 25,765 shares of Class A Common Stock restricted stock awards (the Subject Shares).

The Voting Agreement, and all the rights and obligations of the parties thereunder, may be terminated upon the earliest to occur of
(i) the termination of the Merger Agreement, (ii) the Effective Time, (iii) such time as any amendment to the Merger Agreement is effected without the Shaich Holders consent that decreases the amount or changes the form or
timing of the Merger Consideration or that materially and adversely affects the Shaich Holders, or (iv) by mutual written consent.

The foregoing descriptions of the Merger Agreement and the Voting Agreement do not purport to be complete and are qualified in their entirety
by reference to such agreements. The Merger Agreement and Voting Agreement are referenced herein as Exhibits 2 and 3 and are incorporated by reference into this Item 4.

Item 5. Interest in Securities of the Issuer.

(a) Pursuant to the Voting Agreement, the Reporting Persons may be deemed, for purposes of Rule 13d-3
under the Exchange Act to share with the Shaich Holders the power to vote or to have the power to direct the voting or disposition of the Subject Shares, and thus, for the purpose of said Rule 13d-3, the
Reporting Persons may be deemed to be the beneficial owners of an aggregate of 1,387,214 Shares, which constitutes approximately 6.10% of the Shares, and 15.5% of the voting power of the Shares issued and outstanding. Except as set forth in this
Item 5(a), none of the Reporting Persons, and, to the best knowledge of the Reporting Persons, none of the persons named in Schedule A hereto beneficially owns any Shares. Neither the filing of this Schedule 13D nor any of its contents shall be
deemed to constitute an admission by the Reporting Persons that it is the beneficial owner of any Shares.

See the foregoing descriptions
of the Merger Agreement and Voting Agreement set forth in Item 4, which are incorporated herein by reference. The Merger Agreement and Voting Agreement are referenced herein as Exhibits 2 and 3 and are incorporated by reference into this Item 5.

(b) Except to the extent that it may be deemed to by virtue of the Voting Agreement, none of the Reporting Persons, and to the best
knowledge of the Reporting Persons, none of the persons named in Schedule A hereto, have sole power to vote or direct the vote, shared power to vote or to direct the vote, or sole or shared power to dispose or to direct the disposition of any of the
Shares.

The Reporting Persons may be deemed in certain circumstances to have the shared power with the Shaich Holders to vote or to have
the power to direct the voting or disposition of the 1,387,214 Subject Shares. However, the Reporting Persons are not entitled to any rights as a stockholder of PNRA as to the Subject Shares, except as otherwise expressly provided in the Voting
Agreement.

The Reporting Persons hereby disclaim that they constitute a group (within the meaning of Section 13(d)(3) of the
Exchange Act) with the Shaich Holders and hereby disclaim beneficial ownership of any Shares beneficially owned by the Shaich Holders or any of their affiliates including, without limitation, the Subject Shares.

(c) Except for the Merger Agreement and the Voting Agreement described above, none of the Reporting Persons, and to the best knowledge of the
Reporting Persons, none of the persons named in Schedule A hereto, has effected any transactions in the Shares during the past 60 days.

(d) Except for the Merger Agreement and the Voting Agreement described above, none of the Reporting Persons, and to the best knowledge of the
Reporting Persons, none of the persons named in Schedule A hereto or any other person (except for the Shaich Holders), and no other person (except for the Shaich Holders), has the right to receive or the power to direct the receipt of dividends
from, or the proceeds from the sale of, the securities of PNRA reported herein.

(e) Not applicable.

Item 6. Contracts, Arrangements, Understandings or Relationships with Respect to Securities of the
Issuer.

Other than as described in Items 3, 4 and 5, to the best of the knowledge of the Reporting Persons, there are no contracts,
arrangements, understandings or relationships (legal or otherwise) between any of the Reporting Persons or any person listed on Schedule A hereto, and any person with respect to any securities of PNRA, including, without limitation, the transfer or
voting of any of the securities, finders fees, joint ventures, loan or option arrangements, puts or calls, guarantees of profits, division of profits or loss, or the giving or withholding of proxies or any pledge or contingency, the occurrence
of which would give another person voting or investment power over the securities of PNRA.

Item 7. Material to be Filed as Exhibits.

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.

Dated: April 13, 2017

EXHIBIT INDEX

SCHEDULE A

Rye Parent Corp.

Set forth
below is a list of the directors and executive officers of Rye Parent Corp. as of April 4, 2017, their present principal occupations or employment, and citizenship.

Rye Merger Sub, Inc.

Set forth below is a list of the directors and executive officers of Rye Merger Sub, Inc. as of April 4, 2017, their present principal
occupations or employment, and citizenship.

Rye Parent Holdings Corp.

Set forth below is a list of the directors and executive officers of Rye Parent Holdings Corp. as of April 4, 2017, their present
principal occupations or employment, and citizenship.

Rye Holdings I Inc.

Set forth below is a list of the directors and executive officers of Rye Holdings I Inc. as of April 4, 2017, their present principal
occupations or employment, and citizenship.

JAB Forest B.V.

Set forth below is a list of the directors and executive officers of JAB Forest B.V. as of April 4, 2017, their present principal
occupations or employment, and citizenship.

JAB Holdings B.V.

Set forth below is a list of the directors and executive officers of JAB Holdings B.V. as of April 4, 2017, their present principal
occupations or employment, and citizenship.

JAB Investments S.à r.l.

Set forth below is a list of the directors and executive officers of JAB Investments S.à r.l. as of April 4, 2017, their present
principal occupations or employment, and citizenship.

JAB Holding Company S.à r.l.

Set forth below is a list of the directors and executive officers of JAB Holding Company S.à r.l. as of April 4, 2017, their
present principal occupations or employment, and citizenship.

Donata Holdings B.V.

Set forth below is a list of the directors and executive officers of Donata Holdings B.V. as of April 4, 2017, their present principal
occupations or employment, and citizenship.

Agnaten SE

Set forth below is a list of the directors and executive officers of Agnaten SE as of April 4, 2017, their present principal occupations
or employment, and citizenship.

Lucresca SE

Set forth below is a list of the directors and executive officers of Lucresca SE as of April 4, 2017, their present principal occupations
or employment, and citizenship.