UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D/A

Under the Securities Exchange Act of 1934

(Amendment No. 1)*

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 to be sent.

* The remainder of this cover page shall be filled out for a reporting person’s initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter disclosures provided in a prior cover page.

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).

CUSIP No. 268253101

CUSIP No. 268253101

CUSIP No. 268253101

CUSIP No. 268253101

This Schedule 13D/A is a joint filing pursuant to Rule 13d-1(k)(1) on behalf of each of the Reporting Persons named below.

Item 1. Security and Issuer

This Amendment No. 1 to Schedule 13D relates to the voting common stock, $3.50 par value, of ECB Bancorp, Inc. (the “Issuer”). The address of the Issuer’s principal executive offices is 35050 U. S. Highway 264 East, Engelhard, North Carolina 27824.

Item 2. Identity and Background

Gregory C. Gibbs, Regina Ann Gibbs and Charles G. Gibbs, Jr., are siblings and are co-executors of the Estate of Anna Mae H. Gibbs.

The Estate of Anna Mae H. Gibbs is an estate created following the death of Anna Mae H. Gibbs and under the supervision of the Clerk of Superior Court of Hyde County, North Carolina. The Estate’s mailing address is Post Office Box 39, Engelhard, North Carolina 27824.

Gregory C. Gibbs is the General Manager of Gibbs Store, LLC, a retail hardware business. Its business address is Post Office Box 39, Engelhard, North Carolina 27824.

Regina Ann Gibbs is employed by Gibbs Store, LLC, a retail hardware business. Its business address is Post Office Box 39, Engelhard, North Carolina 27824.

Charles G. Gibbs, Jr. is employed by Darkwoods Farms, LLC, which engages in farming operations. Its business address is Post Office Box 39, Engelhard, North Carolina 27824

Gibbs Store, LLC, and Darkwoods Farms, LLC, each is a limited liability company organized under North Carolina law. Gregory C. Gibbs, Regina Ann Gibbs, and Charles G. Gibbs, Jr., are the sole members and owners of each of those entities.

Item 3. Source and Amount of Funds or Other Consideration

The securities that resulted in each Reporting Person becoming a 5% beneficial owner are those shares that were deemed to have been acquired by each Reporting Person upon the opening of the Estate of Anna Mae H. Gibbs and the qualification in January of 2006 of Gregory C. Gibbs, Regina Ann Gibbs and Charles G. Gibbs, Jr. as co-executors of the estate (the “Co-Executors”).

Item 4. Purpose of Transaction

Item 4 of the Reporting Persons previously filed Schedule 13D is amended in its entirety as follows:

The shares in the Estate of Anna Mae H. Gibbs (the “Estate”) are being held by the Estate for the purpose of administering the Estate of Anna Mae H. Gibbs and making distributions in accordance with the decedent’s will. In the course of administering the Estate, the Reporting Persons may sell a portion of the shares held by the Estate if that becomes necessary for the payment of debts or taxes owed by the Estate or to generate funds for other Estate purposes. The Reporting Persons who act as the Co-Executors for the Estate are fiduciaries who have a duty to act in the best interests of all persons interested in the Estate with as little sacrifice of value as is reasonable under all of the circumstances. Accordingly, the Reporting Persons have an interest in maximizing the value of the shares held by the Estate and acting in the Estate’s best interests as a shareholder of the Issuer.

The Reporting Persons expect to engage in discussions with management, the board of directors, and other shareholders of the Issuer and other relevant parties concerning the business, capitalization, financial condition, operations, governance, strategy, and future plans of the Issuer, which discussions may include proposals that the Reporting Persons believe will increase shareholder value.

At the Issuer’s Annual Meeting of Shareholders held on June 7, 2012, Gregory C. Gibbs, on behalf of the Reporting Persons, made an open statement to the Issuer, its board of directors and management, as well as to other shareholders in attendance at the Annual Meeting, regarding the Reporting Persons’ concern over the recent financial performance of the Issuer and the Issuer’s wholly-owned subsidiary, The East Carolina Bank. The Reporting Persons expressed their dissatisfaction with the performance of executive management, the loss in market value of the Issuer’s common stock, and the rise in salary expense over the last three years, including recent salary increases given to the Issuer’s executive officers in fiscal year 2011 despite the net loss sustained by the Issuer for the 2011 fiscal year. The Reporting Persons requested that the Issuer’s board of directors ask for the resignation of the Issuer’s President and Chief Executive Officer, and failing that, for the Issuer to terminate his employment and ask for his resignation as a director of the Issuer and its subsidiary bank. A copy of the script of the Statement by Gregory C. Gibbs read on behalf of the Reporting Persons at the Annual Meeting is attached hereto as Exhibit 3 and incorporated by reference herein.

Depending on various factors including, without limitation, the Issuer’s financial position and strategic direction, the outcome of the discussions and actions referenced above, actions taken by the board of directors, price levels of the Issuer’s common stock, other investment opportunities available to the Reporting Persons, conditions in the securities market and general economic and industry conditions, the Reporting Persons may in the future take such actions with respect to their investment in the Issuer as they deem appropriate including, without limitation, (i) purchasing additional shares of common stock or selling some or all of their shares of common stock, (ii) voting for or against and expressing support for or against the proposals of the board of directors of the Issuer or other shareholders of the Issuers, (iii) encouraging the Issuer to explore sales or acquisitions of assets or businesses, or extraordinary corporate transactions, such as a merger, and/or (iv) otherwise changing their intention with respect to any and all matters referred to in Item 4 of this Amendment No. 1 to Schedule 13D.

Item 5. Interest in Securities of the Issuer

(a) The aggregate numbers of shares beneficially owned by each Reporting Person, and the percentages of the Issuer’s outstanding common stock represented by those shares, are as follows:

(b) With respect to the aggregate numbers of shares listed in the table above, the number of shares as to which each Reporting Person has sole or shared voting and/or dispositive power are as follows:

(c) During the past 60 days, the sales set forth below in this Item 5(c) were effected by the identified Reporting Person. The Estate of Anna Mae H. Gibbs and Gregory C. Gibbs have not effected any sales of the Issuer’s common stock in the last 60 days. No purchases of the Issuer’s common stock have been made by any of the Reporting Persons in the last 60 days.

The Issuer’s common stock is traded on the NYSE Amex and the above transactions were effected through open market trades.

(d)   Except with respect to shares held by Charles G. Gibbs, Jr. as joint tenants with rights of survivorship with his spouse and by his spouse individually, and except as otherwise set forth in this Amendment No. 1 to Schedule 13D, no other persons are known to have the right to receive, or the power to direct the receipt of, dividends from, or the proceeds from the sale of, the shares beneficially owned by any of the Reporting Persons.

(e)   Not applicable.

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

The shares held by the Estate of Anna Mae H. Gibbs are pledged as collateral to secure a loan made to the Estate by a bank unaffiliated with the Issuer. The Estate is current under all its obligations under the note.

Item 7. Material to Be Filed as Exhibits

Signatures

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: June 7, 2012

Exhibit 2

Joint Filing Agreement

(Pursuant to Rule 13d-1(k) of the Securities Exchange Act of 1934)

The undersigned acknowledge and agree that the foregoing statement on Schedule 13D is filed on behalf of each of the undersigned and that all subsequent amendments to this statement on Schedule 13D may be filed on behalf of each of the undersigned without the necessity of filing additional joint filing agreements. The undersigned acknowledge that each shall be responsible for the timely filing of such amendments, and for the completeness and accuracy of the information concerning him or it contained herein and therein, but shall not be responsible for the completeness and accuracy of the information concerning the others, except to the extent that he or it knows that such information is inaccurate.

Dated: June 7, 2012

Exhibit 3

Script of Statement by Gregory Gibbs at ECB Bancorp Shareholders Meeting

My name is Gregory Gibbs who, along with my family and the estate of my mother, is the largest shareholder of common stock of ECB Bancorp owning more than 13% of the Company. As many of you know, I am a former director of the Company, having resigned in September 2011 after 17 years of service as a member of the board of directors of the bank and the Company. This statement I am about to read has the approval and endorsement of my family, and I suspect that a number of my fellow shareholders may share the same concerns. In short, my family is concerned about the performance of management and the financial results of the Company and we believe a leadership change is needed. In support of this belief, I want to highlight a few facts that I believe are strong evidence of the need for a change in direction of the Company.

Additionally, according to the Company’s proxy statement, the top 3 executives, Messrs. Utz, Crowder, and Burson each received salary increases from 2010 to 2011. Mr. Utz’s salary was increased by $26,425, Mr. Crowder’s salary was increased by $35,000, and Mr. Burson’s increased by $14,583. Collectively, this represents an approximate 13% increase in the top 3 executives’ salaries during 2011 over what was paid in 2010. The total, combined annual compensation during 2011 for these three executives was approximately $826 thousand according to the Company’s proxy statement for this annual meeting. Per the terms of Mr. Utz’s publicly available employment agreement, Mr. Utz agreed to an annual base salary of $259,700 beginning in January of 2010. Yet, since that time, his salary has been increased over 17%, which occurred during a time when the Company lost money in two consecutive years. I simply do not understand this. I am in full support of rewarding management when they produce positive returns for the shareholders, but increasing salaries for the top 3 executives at a time when the Company is losing money seems wrong to me.

Now, let me ask you a question. If I spent almost $2 million of YOUR money on a deal without iron-clad binding agreements from which the other parties could NOT withdraw, would you be happy? Would you TRUST me to lead you? Would you have CONFIDENCE in me?

I ask in open meeting today for the resignation of Mr. Utz, and failing that, for the board of directors to consider terminating Mr. Utz as president and chief executive officer and to ask for his resignation as a director of ECB Bancorp and The East Carolina Bank. Mr. Utz has had three years to assemble his management team and produce the financial results that we as shareholders expect from our investment. Unfortunately, Company management has not performed up to expectations. I trust, as they do with all shareholder requests, that the members of the board of directors will give appropriate consideration to this request and do what is in the best interest of all the shareholders based on the Management team’s record of prior performance.