Exhibit 10.1

AMENDED AND RESTATED

CHIPOTLE MEXICAN GRILL, INC. 2006 CASH INCENTIVE PLAN

(AS ADOPTED MAY 21, 2008)

Section 1. Purpose.

The purpose of the 2006 Cash Incentive Plan (the “Plan”) is to promote the
interests of Chipotle Mexican Grill, Inc. (“Chipotle”) and its subsidiaries (the
“Company”) by providing eligible key employees of the Company with incentive to
assist the Company in meeting and exceeding its business goals.

Section 2. Administration.

(a) The Plan shall be administered by the Executive Compensation Committee (the
“Committee”) of the Board of Directors of Chipotle (the “Board”) from among its
members and shall be comprised of not fewer than two members who shall be
“outside directors” within the meaning of Section 162(m) of the Internal Revenue
Code of 1986, as amended (the “Code”), and the regulations thereunder.

(b) The Committee may, subject to the provisions of the Plan, establish, adopt
or revise rules and regulations relating to the Plan or take such actions as it
deems necessary or advisable for the proper administration of the Plan. The
Committee shall have the authority to interpret the Plan in its discretion. Each
interpretation made or action taken by the Committee pursuant to the Plan shall
be final and conclusive for all purposes and binding upon all Participants (as
defined in Section 3) or former Participants and their successors in interest.

(c) Neither the Committee nor any member of the Committee shall be liable for
any act, omission, interpretation, construction or determination made in good
faith in connection with the Plan, and the members of the Committee shall be
entitled to indemnification and reimbursement by Chipotle in respect of any
claim, loss, damage or expense (including, without limitation, reasonable
attorneys’ fees) arising or resulting therefrom to the fullest extent permitted
by law.

Section 3. Eligibility.

Awards may be granted to key employees of the Company who are selected for
participation in the Plan by the Committee. A qualifying employee selected by
the Committee to participate in the Plan shall be a “Participant” in the Plan.

Section 4. Award Criteria.

The Committee may grant performance-based awards (“Awards”) to Participants with
respect to any performance period (each, a “Performance Period”), subject to the
terms and conditions of the Plan. All Awards shall be settled in cash.
Performance Periods may be equal to or longer than, but not less than, one
fiscal year of the Company and may be overlapping. Within 90 days after the

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

beginning of a Performance Period, and in any case before 25% of the Performance
Period has elapsed, the Committee shall establish (a) performance goals and
objectives (“Performance Targets”) for the Company for such Performance Period,
(b) target awards (“Target Awards”) for each Participant which shall be a
specified dollar amount, and (c) schedules or other objective methods for
determining the applicable performance percentage (“Performance Percentage”) to
be applied to each Target Award to which a Performance Target relates in
arriving at the actual Award payout amount (“Performance Schedules”).

Section 5. Performance Targets.

The Committee shall establish Performance Targets for each Performance Period.
Such Performance Targets shall be based on one or more of the following
Performance Measures (either alone or in any combination, and may be expressed
with respect to the Company or one or more operating units or groups, as the
Committee may determine): revenue growth; cash flow; cash flow from operations;
net income; earnings per share, diluted or basic; earnings per share from
continuing operations, diluted or basic; earnings before interest and taxes;
earnings before interest, taxes, depreciation, and amortization; earnings from
continuing operations; net asset turnover; inventory turnover; capital
expenditures; net income; income from operations; income before income taxes;
gross or operating margin; restaurant-level operating margin; profit margin;
assets; debt; working capital; return on equity; return on net assets; return on
total assets; return on capital; return on investment; return on revenue; net or
gross revenue; comparable restaurant sales; new restaurant openings; market
share; economic value added; cost of capital; expense reduction levels; safety
record; stock price; productivity; customer satisfaction; employee satisfaction;
and total shareholder return. For any Plan Year, Performance Measures may be
determined on an absolute basis or relative to internal goals or relative to
levels attained in years prior to such Plan Year or related to other companies
or indices or as ratios expressing relationships between two or more Performance
Measures.

The measurement of any Performance Targets may exclude the impact of charges for
extraordinary, unusual or non-recurring items (including without limitation
charges for restructurings and discontinued operations), and the cumulative
effects of accounting changes, each as defined by generally accepted accounting
principles and as identified in the Company’s audited financial statements,
including the notes thereto. Any Performance Targets may be used to measure the
performance of Chipotle or a subsidiary of Chipotle as a whole or any business
unit of Chipotle or any subsidiary or any combination thereof, as the Committee
may deem appropriate, or any of the above Performance Targets as compared to the
performance of a group of comparator companies, or a published or special index
that the Committee, in its discretion, deems appropriate.

Section 6. Awards.

(a) Calculation. In the manner required by Section 162(m) of the Code, the
Committee shall, promptly after the date on which the necessary financial and
other information for a particular Performance Period becomes available, certify
the extent to which Performance Targets have been achieved. Using the
Performance Schedule, the Committee shall determine the Performance Percentage
applicable to each Performance Target and multiply the portion of the Target
Award to which the Performance Target relates by such Performance Percentage in
order to arrive at the actual Award payout for such portion.

 

2

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

(b) Discretionary Reduction. The Committee may, in its discretion, reduce or
eliminate the amount of any Award payable to any Participant, based on such
factors as the Committee may deem relevant, but the Committee may not increase
the amount of any Award payable to any Participant above the amount established
in accordance with the relevant Performance Targets. For purposes of clarity,
the Committee may exercise the discretion provided for by the foregoing sentence
in a non-uniform manner among Participants.

(c) Limitation. The amount paid under the Plan to any Participant with respect
to any Award for a Performance Period of one year shall not exceed $5,000,000.
The amount paid under the Plan to any Participant with respect to any Award for
a Performance Period of more than one year shall not exceed $15,000,000. No
Participant shall be eligible to earn Awards for more than three Performance
Periods that end within any single fiscal year of the Company.

(d) Payment. The Company shall pay Awards as soon as administratively practical
following certification by the Committee of the extent to which the applicable
Performance Targets have been achieved and the determination of the actual
Awards in accordance with Section 5 and this Section 6, and in no event more
than two and one half months following the end of the Performance Period to
which such certification relates.

Section 7. General Provisions.

(a) No Rights to Awards or Continued Employment. No employee of the Company
shall have any claim or right to receive Awards under the Plan. Neither the Plan
nor any action taken under the Plan shall be construed as giving any employee
any right to be retained by the Company.

(b) No Limits on Other Awards and Plans. Nothing contained in this Plan shall
prohibit the Company from establishing other special awards or incentive
compensation plans providing for the payment of incentive compensation to
employees of the Company, including any Participants.

(c) Withholding Taxes. The Company shall deduct from all payments and
distributions under the Plan any required federal, state or local governments
tax withholdings.

(d) Unfunded Status of Plan. The Company shall not have any obligation to
establish any separate fund or trust or other segregation of assets to provide
for payments under the Plan. To the extent any person acquires any rights to
receive payments hereunder from the Company, such rights shall be no greater
than those of an unsecured creditor.

(e) Effective Date; Amendment. The Plan was originally adopted by the Board of
Directors on January 25, 2006, and approved by the shareholders of Chipotle on
January 25, 2006, and was amended and restated and approved by the shareholders
of Chipotle on May 21, 2008. The Committee may at any time and from time to time
alter, amend, suspend or terminate the Plan in whole or in part, provided,
however, that any alteration or amendment that requires shareholder approval in
order to allow Awards under the Plan to qualify as “performance-based
compensation” under Section 162(m) of the Code, or to comply with other
applicable laws or regulations, shall be made subject to such shareholder
approval.

 

3

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

(f) Governing Law. The Plan and the rights of all persons under the Plan shall
be construed and administered in accordance with the laws of the State of
Delaware without regard to its conflict of law principles.

(g) Interpretation. The Plan is designed and intended to comply with
Section 162(m) of the Code and all provisions hereof shall be construed in a
manner so to comply.

 

4