EXPLANATORY NOTE

This Amendment No. 3 (this “Amendment”) amends and supplements the Statement on Schedule 13D relating to the Class A Common Stock, par value $0.001 per share (the “Class A Common Stock”), of Jones Energy, Inc., a Delaware corporation (the “Issuer”), filed on August 8, 2013 (as amended by Amendment No. 1 filed on December 18, 2013 and Amendment No. 2 filed on February 12, 2016, the “Initial Schedule 13D”). As amended by this Amendment, the Initial Schedule 13D is referred to herein as the “Schedule 13D” and is filed on behalf of MCP II (Cayman) AIF Jones Intermediate LLC (“AIF Cayman LLC”), MCP II Jones Intermediate LLC (“Jones II LLC”), MCP II (TE) AIF Jones Intermediate LLC (“TE LLC”), MCP II Co-Investment Jones Intermediate LLC (“Co-Invest LLC”), MCP (C) II Jones Intermediate LLC (“C LLC”), MCP II Executive Fund Jones Intermediate LLC (“Executive LLC” and, together with AIF Cayman LLC, Jones II LLC, TE LLC, Co-Invest LLC and C LLC, the “Intermediate LLCs”), MCP II (Cayman) AIF, L.P. (“AIF Fund”), Metalmark Capital Partners II, L.P. (“Metalmark II Fund”), MCP II (TE) AIF, L.P. (“TE Fund”), Metalmark Capital Partners II Co-Investment, L.P.(“Co-Invest Fund”), Metalmark Capital Partners (Silo) II, L.P. (“C Fund”), Metalmark Capital Partners II Executive Fund, L.P. (“Executive Fund” and, together with the AIF Fund, Metalmark II Fund, TE Fund, Co-Invest Fund, C Fund and Executive Fund, the “Metalmark Funds”), Metalmark Capital Partners II GP, L.P. (“Metalmark GP”), Metalmark Capital Holdings LLC (“Metalmark Holdings”) and Metalmark Capital II LLC (“Metalmark Capital II” and, together with the Intermediate LLCs, the Metalmark Funds and Metalmark GP, the “Metalmark Entities”). The Metalmark Entities are referred to in this Schedule 13D collectively as the “Reporting Persons” and individually as a “Reporting Person.” Except as expressly indicated otherwise below, all items from the Initial Schedule 13D are unchanged. Capitalized terms used in this Amendment but not defined in this Amendment shall have the meanings ascribed to such terms in the Initial Schedule 13D.

Item 2. Identity and Background.

Item 2 of the Initial Schedule 13D is hereby amended and restated in its entirety as follows:

(a) – (e)

This Schedule 13D is being jointly filed by the Reporting Persons pursuant to a Joint Filing Agreement attached to the Initial Schedule 13D as Exhibit 1. The names of the Reporting Persons are MCP II (Cayman) AIF Jones Intermediate LLC, MCP II Jones Intermediate LLC, MCP II (TE) AIF Jones Intermediate LLC, MCP II Co-Investment Jones Intermediate LLC, MCP (C) II Jones Intermediate LLC, MCP II Executive Fund Jones Intermediate LLC , MCP II (Cayman) AIF, L.P., Metalmark Capital Partners II, L.P., MCP II (TE) AIF, L.P., Metalmark Capital Partners II Co-Investment, L.P., Metalmark Capital Partners (Silo) II, L.P., Metalmark Capital Partners II Executive Fund, L.P., Metalmark Capital Partners II GP, L.P., Metalmark Capital Holdings LLC and Metalmark Capital II LLC.

The Reporting Persons have entered into a Joint Filing Agreement, dated February 12, 2016, which is attached as Exhibit 1 to the Initial Schedule 13D and is incorporated into this Item 2 by reference, pursuant to which the Reporting Persons have agreed to file this statement jointly in accordance with the provisions of Rule 13d-1(k)(1) under the Act. As a result of the existing relationships described under this Item 2 and the facts and circumstances described in Items 3, 4, 5 and 6, the Reporting Persons may be deemed to constitute a “group” within the meaning of Rule 13d-5(b) under the Act. However, neither the present filing nor anything contained herein shall be construed as an admission that all or any of the Reporting Persons constitute a “group” within the meaning of Rule 13d-5(b) under the Act. Information with respect to each Reporting Person is given solely by such Reporting Person, and no Reporting Person assumes responsibility for the accuracy or completeness of the information furnished by another Reporting Person.

None of the Reporting Persons directly own any shares of Class A Common Stock and are reporting persons solely by virtue of their direct or indirect ownership of Class B Common Stock of the Issuer (the “Class B Common Stock”) and membership interests (“JEH LLC Units”) of Jones Energy Holdings, LLC (“JEH LLC”) and indirect ownership of Class A Common Stock through Metalmark Management II LLC (“Management LLC”), a wholly-owned indirect subsidiary of Metalmark Capital II. Pursuant to an exchange agreement entered into on July 29, 2013 (the “Exchange Agreement”) among certain of the Reporting Persons’ affiliated investment funds (the “Affiliated Funds”), the Issuer, JEH LLC, Jones Energy Drilling Fund, LP and certain of its affiliated investment funds (the “Jones Family Entities”), Wells Fargo Central Pacific Holdings, Inc. (together with the Affiliated Funds and the Jones Family Entities, the “Existing Owners”), the Existing Owners (and certain permitted transferees) may (subject to the terms of the Exchange Agreement), exchange their JEH LLC Units (and a corresponding number of shares of Class B Common Stock) for shares of Class A Common Stock (on a one-for-one basis, subject to customary conversion rate adjustments for stock splits, stock dividends and reclassification and other similar transactions). The Exchange Agreement is attached to the Initial Schedule 13D as Exhibit 2 and incorporated by reference in its entirety into this Item 2.

Each of the Intermediate LLCs, Metalmark Holdings and Metalmark Capital II is a Delaware limited liability company. Each of the Metalmark Funds and Metalmark GP is a Delaware limited partnership.

Each of the Reporting Persons (directly or indirectly through subsidiaries or affiliated companies or both) is principally engaged in the business of investing in equity, debt, derivative and other securities and assets. AIF Fund is the sole member of AIF Cayman LLC. Metalmark II Fund is the sole member of Jones II LLC. TE Fund is the sole member of TE LLC. Co-Invest Fund is the sole member of Co-Invest LLC. C Fund is the sole member of C LLC. Executive Fund is the sole member of Executive LLC. Metalmark GP is the general partner of each of the Metalmark Funds. Metalmark Holdings is the general partner of Metalmark GP. Metalmark Capital II is the sole member of Metalmark Holdings.

The principal address of each Reporting Person is 1177 Avenue of the Americas, 40th Floor, New York, NY 10036. Set forth in Schedule A attached hereto and incorporated herein by reference is a listing of the members and executive officers of Metalmark Capital II and the business address, present principal occupation or employment and citizenship of each such person.

During the past five years, none of the Reporting Persons nor any person listed on Schedule A attached hereto has been (i) convicted in a criminal proceeding (excluding traffic violations or similar misdemeanors), or (ii) 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.

This Item 2 is qualified in its entirely by reference to Schedule A attached hereto, which is incorporated into this Item 2 by reference.

Item 4. Purpose of the Transaction.

Item 4(a) of the Initial Schedule 13D is hereby amended and supplemented by adding the following information:

No acquisition of Class A Common Stock by the Reporting Persons has occurred since the date of the Initial Schedule 13D. The Reporting Persons are filing this Amendment to report the acquisition of 200,000 shares of the Issuer’s 8.0% Series A Perpetual Convertible Preferred Stock, par value $0.001, by certain affiliates of the Reporting Persons. The Reporting Persons have no other plans or proposals to acquire additional securities of the Issuer or to dispose of any securities of the Issuer.

Item 5. Interest in Securities of the Issuer.

Item 5 of the Initial Schedule 13D is hereby amended and restated in its entirety as follows:

(a) The Reporting Persons may be deemed to constitute a “group” within the meaning of Rule 13d-5(b) under the Act as a result of the facts and circumstances described in Items 2, 3, 4, 5 and 6 of this Schedule 13D. For purposes of Rule 13d-3 of the Act, the Reporting Persons as a group may be deemed to beneficially own in the aggregate 18,311,360 shares of Class A Common Stock, representing 25.4% of the Class A Common Stock, based on the number of shares of Class A Common Stock (53,819,222) issued and outstanding as of August 23, 2016, as reported in the Issuer’s prospectus supplement filed on August 23, 2016, and assuming all outstanding JEH LLC Units (18,204,216) beneficially owned by the Reporting Persons as of February 12, 2016 (and no other outstanding JEH LLC Units) were exchanged (along with a corresponding number of shares of Class B Common Stock) (the “Exchange”) for newly-issued shares of Class A Common Stock. The Reporting Persons do not directly own any shares of Class A Common Stock.

(b) AIF Cayman LLC directly owns and has the shared power to vote, direct the voting of, dispose of and direct the disposition of 2,973,397 shares of Class B Common Stock and 2,973,397 JEH LLC Units, representing 4.1% of the Class A Common Stock assuming the occurrence of the Exchange. By virtue of the relationship previously reported under Item 2 of this Schedule 13D, AIF Fund may be deemed to beneficially own and have shared power to vote, direct the voting of, dispose of and direct the disposition of the shares of Class B Common Stock and JEH LLC Units owned by AIF Cayman LLC, representing 4.1% of the Class A Common Stock assuming the occurrence of the Exchange.

Jones II LLC directly owns and has the shared power to vote, direct the voting of, dispose of and direct the disposition of 3,357,483 shares of Class B Common Stock and 3,357,483 JEH LLC Units, representing 4.7% of the Class A Common Stock assuming the occurrence of the Exchange. By virtue of the relationship previously reported under Item 2 of this Schedule 13D, the Metalmark II Fund may be deemed to beneficially own and have shared power to vote, direct the voting of, dispose of and direct the disposition of the shares of Class B Common Stock and JEH LLC Units owned by Jones II LLC, representing 4.7% of the Class A Common Stock assuming the occurrence of the Exchange.

TE LLC directly owns and has the shared power to vote, direct the voting of, dispose of and direct the disposition of 2,570,033 shares of Class B Common Stock and 2,570,033 JEH LLC Units, representing 3.6% of the Class A Common Stock assuming the occurrence of the Exchange. By virtue of the relationship previously reported under Item 2 of this Schedule 13D, the TE Fund may be deemed to beneficially own and have shared power to vote, direct the voting of, dispose of and direct the disposition of the shares of Class B Common Stock and JEH LLC Units owned by TE LLC, representing 3.6% of the Class A Common Stock assuming the occurrence of the Exchange.

Co-Invest LLC directly owns and has the shared power to vote, direct the voting of, dispose of and direct the disposition of 1,791,914 shares of Class B Common Stock and 1,791,914 JEH LLC Units, representing 2.5% of the Class A Common Stock assuming the occurrence of the Exchange. By virtue of the relationship previously reported under Item 2 of this Schedule 13D, the Co-Invest Fund may be deemed to beneficially own and have shared power to vote, direct the voting of, dispose of and direct the disposition of the shares of Class B Common Stock and JEH LLC Units owned by Co-Invest LLC, representing 2.5% of the Class A Common Stock assuming the occurrence of the Exchange.

C LLC directly owns and has the shared power to vote, direct the voting of, dispose of and direct the disposition of 7,182,989 shares of Class B Common Stock and 7,182,989 JEH LLC Units, representing 10.0% of the Class A Common Stock assuming the occurrence of the Exchange. By virtue of the relationship previously reported under Item 2 of this Schedule 13D, the C Fund may be deemed to beneficially own and have shared power to vote, direct the voting of, dispose of and direct the disposition of the shares of Class B Common Stock and JEH LLC Units owned by C LLC, representing 10.0% of the Class A Common Stock assuming the occurrence of the Exchange.

Executive LLC directly owns and has the shared power to vote, direct the voting of, dispose of and direct the disposition of 328,400 shares of Class B Common Stock and 328,400 JEH LLC Units, representing 0.5% of the Class A Common Stock assuming the occurrence of the Exchange. By virtue of the relationship previously reported under Item 2 of this Schedule 13D, the Executive Fund may be deemed to beneficially own and have shared power to vote, direct the voting of, dispose of and direct the disposition of the shares of Class B Common Stock and JEH LLC Units owned by Executive LLC, representing 0.5% of the Class A Common Stock assuming the occurrence of the Exchange.

By virtue of the relationships previously reported under Item 2 of this Schedule 13D, each of Metalmark GP and Metalmark Holdings may be deemed to beneficially own and have shared power to vote, direct the voting of, dispose of and direct the disposition of the shares of Class B Common Stock and JEH LLC Units owned by the Intermediate LLCs, representing 25.3% of the Class A Common Stock assuming the occurrence of the Exchange.

By virtue of (i) the relationships previously reported under Item 2 of this Schedule 13D, through which Metalmark Capital II may be deemed to beneficially own and have shared power to vote, direct the voting of, dispose of and direct the disposition of the shares of Class B Common Stock and JEH LLC Units owned by the Intermediate LLCs, (ii) ownership by Management LLC, a wholly-owned indirect subsidiary of Metalmark Capital II, of 51,214 shares of Class A Common Stock and (iii) the ownership of restricted Class A Common Stock by Howard I. Hoffen and Gregory Myers described below, Metalmark Capital II may be deemed to beneficially own and have shared power to vote, direct the voting of, dispose of and direct the disposition of 25.4% of the Class A Common Stock assuming the occurrence of the Exchange.

Howard I. Hoffen holds 27,965 restricted shares of Class A Common Stock granted by the Issuer to Mr. Hoffen in respect of his service on the Issuer’s board of directors. Mr. Hoffen is a Partner of Management LLC. These securities will fully vest on May 25, 2017. In connection with the vesting of these securities, Mr. Hoffen will assign all rights, title and interest in these securities to Management LLC.

Gregory Myers holds 27,965 restricted shares of Class A Common Stock granted by the Issuer to Mr. Myers in respect of his service on the Issuer’s board of directors. Mr. Myers is a Partner of Management LLC. These securities will fully vest on May 25, 2017. In connection with the vesting of these securities, Mr. Myers will assign all rights, title and interest in these securities to Management LLC.

In addition to the beneficial ownership of the Reporting Persons described herein, by virtue of the Stockholders Agreement filed with the Initial Schedule 13D and incorporated herein by reference, each of the Reporting Persons, together with the Jones Family Entities, may be deemed to be a member of a “group” under Section 13(d) of the Act, which may be deemed to beneficially own, have shared power to vote or direct the vote over and have shared dispositive power over 11,668,210 shares of Class A Common Stock beneficially owned by the Jones Family Entities, as reported in the Jones Family Entities’ Statement on Schedule 13D filed on May 9, 2014, as amended. The Reporting Persons disclaim beneficial ownership of the Class A Common Stock beneficially owned by the Jones Family Entities.

The information set forth in Items 7 through 11 of the cover pages hereto are incorporated herein by reference. Neither the filing of this Schedule 13D nor any of its contents shall be deemed to constitute an admission by any of the Reporting Persons that it is the beneficial owner of any of the Class A Common Stock referred to herein for the purposes of Section 13(d) of the Act or for any other purpose, and such beneficial ownership is expressly disclaimed by each Reporting Person except to the extent of such Reporting Person’s pecuniary interest, if any, in the Class A Common Stock.

(c) Except as set forth in this Schedule 13D, none of the Reporting Persons has effected any transactions in Common Units in the past 60 days.

(d) No other person is known by the Reporting Persons to have the right to receive or the power to direct the receipt of dividends from, or the proceeds from the sale of, the Class A Common Stock that may be deemed to be beneficially owned by the Reporting Persons as provided for herein.

(e) As a result of certain transactions by the Issuer, each of MCP II Co-Investment Jones Intermediate LLC, MCP II Jones Intermediate LLC, MCP II (TE) AIF Jones Intermediate LLC, MCP II (Cayman) AIF Jones Intermediate LLC, MCP II Executive Fund Jones Intermediate LLC, MCP II (Cayman) AIF, L.P., Metalmark Capital Partners II, L.P., MCP II (TE) AIF, L.P., Metalmark Capital Partners II Co-Investment, L.P. and Metalmark Capital Partners II Executive Fund, L.P. have ceased to beneficially own 5% or more of the outstanding shares of Class A Common Stock.

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: September 9, 2016

SCHEDULE A

Members and Executive Officers of Metalmark Capital II LLC

Schedule A is hereby amended and restated in its entirety as follows:

The following sets forth the name, principal occupation and citizenship of each of the members and executive officers of Metalmark Capital II LLC. The business address of each of the persons listed below is 1177 Avenue of the Americas, 40th Floor, New York, NY 10036.