Exhibit 10.1

THIRD AMENDMENT TO

CLEVELAND BIOLABS, INC.

EQUITY INCENTIVE PLAN

1. Section 1 (Establishment and Purpose) of the Cleveland BioLabs, Inc. Equity
Incentive Plan (the “Plan”) is hereby deleted in its entirety and replaced with
the following:

The Cleveland BioLabs, Inc. Equity Incentive Plan (the “Plan”) was established
under the name Cleveland BioLabs, Inc. 2006 Equity Incentive Plan (the “2006
Plan”) by Cleveland BioLabs, Inc., a Delaware corporation (the “Company”). The
Plan was amended, restated and renamed upon its approval by the Company’s
stockholders effective April 29, 2008, and amended by the First Amendment to the
Plan upon its approval by the Company’s stockholders effective June 8, 2010 and
by the Second Amendment to the Plan upon its approval by the Company’s
stockholders effective June 13, 2012. The Plan is hereby further amended, as set
forth herein, effective April 14, 2014, subject to the approval of the Company’s
stockholders of that certain Third Amendment (the “Third Amendment”) to the
Plan. The purpose of the Plan is to attract and retain persons eligible to
participate in the Plan; motivate Participants to achieve long-term Company
goals; and further align Participants’ interests with those of the Company’s
other stockholders. No Awards that are settled in Stock shall be granted
hereunder prior to the approval of the Plan by the Company’s stockholders.
Unless the Plan is discontinued earlier by the Board as provided herein, no
Award shall be granted hereunder on or after the date 10 years after the
Effective Date. The Plan shall terminate on April 29, 2018, or such earlier time
as the Board may determine.

2. The first paragraph of Section 3 (Stock Subject to Plan) of the Plan is
hereby deleted in its entirety and replaced with the following:

Subject to adjustment as provided in this Section 3, the number of shares of
Stock reserved for delivery under the Plan shall be the sum of (a) three hundred
thousand (300,000) shares, plus (b) the number of remaining shares under the
2006 Plan and the Plan, as amended, (i.e., not subject to outstanding Awards and
not delivered out of shares reserved thereunder) as of the date of stockholder
approval of that certain Second Amendment to the Plan, as amended, plus (c) the
number of shares that become available under the 2006 Plan or the Plan, as
amended, after the date of stockholder approval of the Second Amendment pursuant
to forfeiture, termination, lapse or satisfaction of an Award in cash or
property other than shares, application as payment for an Award, or, except with
respect to Restricted Stock, to satisfy withholding, plus (d) any shares
required to satisfy Substitute Awards.

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3. The third paragraph of Section 3 (Stock Subject to Plan) of the Plan is
hereby deleted in its entirety and replaced with the following:

Subject to adjustment as provided in this Section 3, the maximum number of
shares that may be covered by Stock Options, Stock Appreciation Rights, Stock
Awards and Performance Awards payable in Shares, in the aggregate, granted to
any one Participant during any calendar year shall be one hundred thousand
(100,000) shares. No Participant may be granted a Performance Award payable in
cash, the maximum payout for which would exceed one million dollars ($1,000,000)
during any calendar year. No Participant may be granted a Performance Award for
a Performance Period of more than one (1) Year, the maximum payout for which
would exceed two and one-half million dollars ($2,500,000).

4. The foregoing amendment was duly adopted and approved in accordance with
Section 9(a) of the Plan.