13D Filing: Mill Road Capital Ii, L.p. and Noodles & Co (NASDAQ:NDLS)

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No.    )*

Noodles & Company

(Name of Issuer)

Class A Common Stock, $0.01 par value

(Title of Class of Securities)

65540B105

(CUSIP Number)

Mill Road Capital II, L.P.

Attn: Thomas E. Lynch

382 Greenwich Avenue

Suite One

Greenwich, CT
06830

203-987-3500

With a copy to:

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

March 13, 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 §§240.13d-1(e), 240.13d-1(f) or 240.13d-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 §240.13d-7 for
other parties to whom copies are sent.

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 joint statement on Schedule 13D relates to the Class A common stock, par
value $0.01 (the Common Stock), of Noodles & Company, a Delaware corporation (the Issuer). The address of the Issuers principal executive offices is 520 Zang Street, Suite D, Broomfield, Colorado
80021.

(a) This joint statement on Schedule 13D is being filed by
Thomas E. Lynch, Scott P. Scharfman, Mill Road Capital II GP LLC, a Delaware limited liability company (the GP), and Mill Road Capital II, L.P., a Delaware limited partnership (the Fund). Each of the foregoing
is referred to in this Schedule 13D as a Reporting Person and, collectively, as the Reporting Persons. Messrs. Lynch and Scharfman and Justin C. Jacobs are the management committee directors of the GP and, in
this capacity, are referred to in this Schedule 13D as the Managers. The GP is the sole general partner of the Fund. Each of Messrs. Lynch and Scharfman has shared authority to vote and dispose of the shares of Common Stock
reported in this Schedule 13D.

The Reporting Persons have entered into a Joint Filing Agreement dated March 23, 2017, a copy of
which is filed as Exhibit 1 to this Schedule 13D, pursuant to which they have agreed to file this Schedule 13D jointly in accordance with Rule 13d-1(k) under the Securities Exchange Act of 1934, as amended (the Exchange
Act).

(b) The business address of each of the Managers, and the address of the principal business and the principal office of
the GP and the Fund, is 382 Greenwich Avenue, Suite One, Greenwich, Connecticut 06830.

(c) The principal business of the GP is acting as
the sole general partner of the Fund. The principal business of the Fund is investing in securities. The present principal occupation or employment of each Manager is as a management committee director of the GP and of Mill Road Capital Management
LLC, a Delaware limited liability company (the Management Company), which provides advisory and administrative services to the GP and is located at 382 Greenwich Avenue, Suite One, Greenwich, Connecticut 06830.

(d) None of the Managers, the GP and the Fund has, during the last five years, been convicted in a criminal proceeding (excluding traffic
violations or similar misdemeanors).

(e) None of the Managers, the GP and the Fund was, during the last five years, 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 (1) enjoining future violations of, or prohibiting or mandating activities
subject to, federal or state securities laws, or (2) finding any violation with respect to such laws.

(f) Each Manager is a citizen
of the United States.

The Reporting Persons acquired beneficial ownership
of an aggregate of 8,873,240 shares of Common Stock for consideration to be paid at closing that will consist of approximately $31.5 million of cash, which is expected to be drawn from working capital from the Fund. The Reporting Persons acquired
beneficial ownership of such shares pursuant to a Securities Purchase Agreement (the Purchase Agreement) entered into between the Fund and the Issuer on March 13, 2017. The Purchase Agreement is attached hereto as Exhibit
4 and more fully described in Item 6 below.

The Reporting Persons acquired shares of the Common Stock based on their belief
that the Common Stock represents an attractive investment opportunity. The following information may be deemed pertinent.

As more fully described in
Item 6 below, on March 13, 2017, the Fund and the Issuer entered into the Purchase Agreement pursuant to which the Fund agreed to purchase, on April 3, 2017 or such other date and time as the parties might agree, 8,873,240 shares of
Common Stock. Consummation of the purchase is subject to customary closing conditions.

The Reporting Persons intend to review continuously their
investment in the Issuer. Depending upon their evaluation of the factors described below, one or more of the Reporting Persons may from time to time (with the consent of the Issuer, if required) purchase additional securities of the Issuer, dispose
of all or a portion of the securities then held by such Reporting Persons, or cease buying or selling such securities; any such additional purchases or sales of securities of the Issuer may be in the open market, in privately negotiated transactions
or otherwise.

The Reporting Persons may wish to engage in a constructive dialogue with officers, directors and other representatives of the Issuer, as
well as the Issuers shareholders; topics of discussion may include, but are not limited to, the Issuers markets, operations, competitors, prospects, strategy, personnel, directors, ownership and capitalization. The Reporting Persons may
also enter into or amend confidentiality or similar agreements with the Issuer and, subject to such an agreement or otherwise, exchange information with the Issuer. The factors that the Reporting Persons may consider in evaluating their investment
in the Issuers business include the following: (i) the Issuers business and prospects; (ii) the performance of the Common Stock and the availability of the Common Stock for purchase at particular price levels; (iii) the
availability and nature of opportunities to dispose of the Reporting Persons interests; (iv) general economic conditions; (v) stock market conditions; (vi) other business and investment opportunities available to the Reporting
Persons; and (vii) other plans and requirements of the Reporting Persons.

Depending on their assessment of the foregoing factors, the Reporting
Persons may, from time to time, modify their present intention as stated in this Item 4.

Except as set forth above and as described in Item 6
below, which is hereby incorporated by reference into this Item 4, the Reporting Persons intend to continuously review their options but do not have at this time any specific plans that would result in (a) the acquisition of additional
securities of the Issuer or the disposition of securities of the Issuer; (b) any extraordinary

corporate transactions such as a merger, reorganization or liquidation involving the Issuer or any of its subsidiaries; (c) any sale or transfer of a material amount of the assets of the
Issuer or of any of its subsidiaries; (d) any change in the present management or Board of Directors of the Issuer, including any plans or proposals to change the number or term of directors or to fill any existing vacancies on the
Issuers Board of Directors; (e) any material change in the present capitalization or dividend policy of the Issuer; (f) any other material change in the Issuers business or corporate structure; (g) any change in the
Issuers charter or by-laws or other action that may impede the acquisition of control of the Issuer by any person; (h) the Issuers Common Stock being delisted from a national securities exchange or ceasing to be authorized to be
quoted in an inter-dealer quotation system or a registered national securities association; (i) causing a class of equity securities of the Issuer to become eligible for termination of registration pursuant to Section 12(g)(4) of the
Securities Exchange Act of 1934, as amended; or (j) any action similar to those enumerated above.

(a, b) The percentages of beneficial ownership
reported in this Item 5, and on each Reporting Persons cover page to this Schedule 13D, are based on a total of 35,224,067 shares of Common Stock, consisting of the sum of (i) 26,350,827 shares of Common Stock issued and outstanding
as of February 24, 2017, as reported in the Issuers annual report on Form 10-K for the fiscal year ended January 3, 2017 and (ii) 8,873,240 shares of Common Stock to be issued to the Fund pursuant to the Purchase Agreement. All
of the share numbers reported below, and on each Reporting Persons cover page to this Schedule 13D, are as of March 23, 2017, unless otherwise indicated. The cover page to this Schedule 13D for each Reporting Person is incorporated by
reference in its entirety into this Item 5(a, b).

As a result of the receipt of certain consents and waivers on March 13, 2017,
which consents and waivers are conditions to the consummation of the purchase by the Fund of 8,873,240 shares of Common Stock pursuant to the Purchase Agreement, each of the Fund, the GP and Messrs. Lynch and Scharfman may be deemed to have acquired
beneficial ownership of such shares on that date.

Accordingly, each of the Reporting Persons beneficially owns or may be deemed to
beneficially own an aggregate of 8,873,240 shares of Common Stock, or approximately 25.2% of the outstanding shares of Common Stock, and the Reporting Persons beneficially own or may be deemed to beneficially own, in the aggregate, 8,873,240 shares
of Common Stock, or approximately 25.2% of the outstanding shares of Common Stock.

(c) As of March 13, 2017, each of the Reporting
Persons may be deemed to have acquired beneficial ownership of 8,873,240 shares of Common Stock as a result of the satisfaction of certain conditions, set forth in the Purchase Agreement, to the consummation by the Fund of the purchase of such
shares. Except as set forth in the preceding sentence, no Reporting Person effected any transaction in shares of the Common Stock from January 22, 2017 (the date 60 days prior to the filing of this Schedule 13D) to March 23, 2017.

(d) No person other than the Reporting Persons 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 shares of the Common Stock.

(e) Not applicable.

The
following description of certain agreements and other documents does not purport to be complete and is qualified in its entirety by reference to the terms and conditions of such agreements and other documents, copies of which are filed as
Exhibits 4 and 5 to this Schedule 13D and are incorporated by reference in their entirety into this Item 6.

The Purchase Agreement

The Purchase Agreement provides for the issuance and sale by the Issuer to the Fund of 8,873,240 shares of Common Stock (the
Shares). The base purchase price for the Shares is $3.55 per share, or an aggregate of $31,500,002, which will be paid at the closing of the transactions contemplated by the Purchase Agreement.

The Purchase Agreement contains customary representations, warranties, covenants and agreements. The consummation of the transactions contemplated by the
Purchase Agreement is subject to the satisfaction of certain conditions, including certain consents and the waiver of certain rights pursuant to (i) a securities purchase agreement between the Issuer and a stockholder of the Issuer,
Catterton-Noodles, LLC (Catterton), (ii) a stockholders agreement among the Issuer and certain stockholders of the Issuer, including Catterton and Argentia Private Investments, Inc. (Argentia), and
(iii) a registration rights agreement among the Issuer and certain stockholders of the Issuer, including Catterton and Argentia. Certain consents and waivers were received on March 13, 2017. The Purchase Agreement provides that the Issuer
is obligated to indemnify the Fund and its affiliates under certain circumstances based upon (i) breaches by the Issuer of its representations, warranties, covenants or agreements in the Purchase Agreement, (ii) any untrue or alleged
untrue statements of a material fact contained in any registration statement filed pursuant to certain registration rights granted by the Issuer to the Fund in the Purchase Agreement, and (iii) certain third-party claims brought in connection
with the transactions contemplated under the Purchase Agreement or any transaction financed by the proceeds of the sale of the Shares.

Under the terms of
the Purchase Agreement, the Fund is entitled, subject to maintaining a minimum threshold of ownership in the Common Stock, to designate one nominee to the Board of Directors of the Issuer. The Reporting Persons expect that, in connection with the
closing of the transactions contemplated by the Purchase Agreement, the Fund will designate Mr. Lynch as its nominee to the Board of Directors of the Issuer.

In addition, the Issuer has agreed to file a Form S-3 or similar short-form registration statement to register the resale of the Shares within sixty
(60) days after the closing of the transactions contemplated by the Purchase Agreement. The Purchase Agreement also extended the term of the standstill provision contained in the Side Letter, as defined and further described below.

The Side Letter

On February 15, 2017, the Issuer entered into a letter agreement with the Management Company (the Side Letter) in connection with the
negotiation and discussion of a possible minority equity investment in the Issuer. In addition to obligations of confidentiality and non-solicitation, the Management Company generally agreed, among other things, not to acquire additional equity
securities of the Issuer for a period of one year following the date of the Side Letter. The Purchase Agreement extended the term of this standstill provision from one year to two years following the date of the Side Letter.

Except as otherwise described in this Schedule 13D, including the Exhibits attached hereto, there are no contracts, arrangements, understandings, or
relationships (legal or otherwise) among the Reporting Persons, or between any Reporting Person(s) and any third party, with respect to any securities of the Issuer, including, but not limited to, those involving the transfer or voting of any of
such securities, finders fees, joint ventures, loan or option arrangements, put or calls, guarantees of profits, division of profits or losses, or the giving or withholding of proxies.

[signature pages follow]

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.