U. S. SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D. C. 20549

FORM 10-K/A

(Amendment No. 1)

For the fiscal year ended December 31, 2012

For the transition period from                      to                     

Commission File Number 0-11255

HERITAGE BANKSHARES, INC.

(Exact name of registrant as specified in its charter)

Registrant’s telephone number (757) 648-1700

Securities registered pursuant to Section 12(b) of the Exchange Act: None

Securities registered pursuant to Section 12(g) of the Exchange Act: Common Stock, $5.00 par value

Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Section 405 of the Securities Act.    Yes  ¨    No  x

Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or 15(d) of the Exchange Act.    Yes  ¨    No  x

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.    Yes  x    No  ¨

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).    Yes  x    No  ¨

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of registrant’s knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K.    ¨

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one):

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).    Yes  ¨    No  x

The aggregate market value of the registrant’s Common Stock held by non-affiliates of the registrant as of June 30, 2012 was approximately $20,212,000. Aggregate market value was computed by reference to the sales price of the Common Stock of the registrant on June 30, 2012 of $12.20 per share and 1,656,714 shares of voting stock held by non-affiliates of the registrant on that date.

As of February 28, 2013, 2,276,617 shares of Common Stock of the registrant, par value $5.00 per share were issued and outstanding.

EXPLANATORY NOTE

This Amendment No. 1 on Form 10-K/A (this “Amendment”) amends the Annual Report on Form 10-K of Heritage Bankshares, Inc. (the “Company”) for the fiscal year ended December 31, 2012, which was filed with the Securities and Exchange Commission on March 29, 2013 (the “2012 Annual Report”).

This Amendment is being filed solely to update the Summary Compensation Table set forth in Item 11 of the 2012 Annual Report to include certain compensation that was inadvertently omitted from the original filing. In addition, as required by Rule 12b-15 promulgated under the Securities Exchange Act of 1934, as amended (the “Exchange Act”), new certifications by our principal executive officer and principal financial officer are filed as exhibits to this Amendment. Pursuant to Rule 12b-15 promulgated under the Exchange Act, the complete text of Part III, Item 11, and Part IV, Item 15, as amended, are set forth in this Amendment.

Except as described above, no other changes have been made to the 2012 Annual Report. This Amendment to the 2012 Annual Report has not been updated to reflect events occurring subsequent to the original filing date of the 2012 Annual Report.

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Compensation

The summary compensation table below presents information related to the compensation the Company’s Principal Executive Officer and other Named Executive Officers received during the fiscal years ended December 31, 2012 and 2011:

Summary Compensation Table for the Fiscal Years Ended December 31, 2012 and 2011

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Equity Grants in Last Fiscal Year

In 2006 the Company adopted the Heritage 2006 Equity Incentive Plan, as amended (“2006 Incentive Plan”), which authorizes the grant by the Board of Directors of stock options, stock appreciation rights, restricted stock and certain other equity awards to key employees and nonemployee directors of the Company and the Bank. In connection with the adoption of the 2006 Incentive Plan, the Board of Directors terminated the Company’s ability to issue new awards under both its 1987 Stock Option Plan and its 1999 Stock Option Plan. Awards granted under the 2006 Incentive Plan vest or become exercisable, as applicable, earlier upon a change in control (as defined in the 2006 Incentive Plan) of the Company, and such awards may in certain circumstances also vest or become exercisable, as applicable, earlier upon the grantee’s disability or death, retirement, termination without cause or resignation for good reason.

In 2012, the Board approved the following grants of restricted stock awards to its named executive officers under the 2006 Incentive Plan:

The shares of restricted stock will vest over five (5) years, at the rate of 20% per year, subject to accelerated vesting in limited circumstances. Until the shares of restricted stock vest, they may not be sold, transferred, pledged, assigned or otherwise disposed. In the event of the grantee’s termination of employment for any reason other than death, permanent disability or retirement, all unvested shares of restricted stock shall be automatically forfeited. See the “Outstanding Equity Awards” table below for additional information regarding the year-end market value of such shares of restricted stock.

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Outstanding Equity Awards at 2012 Fiscal Year-End

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Agreements with Named Executive Officers

Employment Contracts

Michael S. Ives. The Company, the Bank and Michael S. Ives, the Company’s President & Chief Executive Officer, entered into an Amended and Restated Employment Agreement dated January 25, 2012. Mr. Ives’ Employment Agreement contains the following material provisions: (i) Mr. Ives’ current term of employment continues until January 31, 2018; (ii) the base salary payable to Mr. Ives under the Employment Agreement is $400,000 per year; and (iii) Mr. Ives is eligible to receive an annual incentive bonus based on performance during the applicable year, as determined by the Board of Directors in its discretion, but no annual bonus may exceed 35% of the base salary paid to Mr. Ives during the applicable year.

John O. Guthrie. The Company, the Bank and John O. Guthrie, the Company’s Executive Vice President & Chief Financial Officer, entered into a new Employment Agreement dated January 1, 2011, which replaced in its entirety Mr. Guthrie’s prior employment agreement immediately following the expiration of such prior agreement on April 30, 2011. This Employment Agreement (i) renewed at year-end 2012 and now continues through December 31, 2014, thereafter renewing automatically for successive additional two-year periods unless the Company or Mr. Guthrie otherwise notifies the other in accordance with the terms of the agreement; and (ii) provides for a base salary that is subject to review, at least annually, and increase by the Company in its sole discretion.

Sharon Curling Lessard. The Bank and Sharon Curling Lessard, the Company’s Executive Vice President & Chief Banking Officer, entered into a new Employment Agreement dated January 1, 2011, which replaced in its entirety a pre-existing employment agreement. This Employment Agreement provides for a base salary that is subject to review, at least annually, and increase by the Company in its sole discretion. Ms. Lessard’s Employment Agreement renewed at year-end 2012; however, she is currently on leave and her employment status is “inactive”.

Leigh C. Keogh. The Bank and Leigh C. Keogh, the Company’s Executive Vice President & Chief Lending Officer, entered into a new Employment Agreement dated January 1, 2011, which replaced in its entirety a pre-existing employment agreement. This Employment Agreement (i) renewed at year-end 2012 and now continues through December 31, 2014, thereafter renewing automatically for successive additional two-year periods unless the Bank or Mr. Keogh otherwise notifies the other in accordance with the terms of the agreement; and (ii) provides for a base salary that is subject to review, at least annually, and increase by the Company in its sole discretion.

Payments Upon Termination of Employment or Change in Control

Mr. Ives. Mr. Ives’ Amended and Restated Employment Agreement also provides for certain payments to Mr. Ives in the following events of termination of his employment: (i) Mr. Ives will continue to receive his base salary for the remainder of the term of his agreement following his termination by the Company without “cause” (as defined in the agreement), except for termination without cause within 12 months after a “change of control” (as defined in the agreement), together with payment for all accrued and unused vacation and sick leave; (ii) Mr. Ives will continue to receive his base salary for the remainder of the term of his agreement following his termination for “good reason” (as defined in the agreement), except for termination for good reason within 12 months after a change in control, together with payment for all accrued and unused vacation and sick leave; (iii) if within 12 months after a change of control Mr. Ives’ employment is terminated without cause or Mr. Ives resigns for good reason, Mr. Ives will receive a lump-sum severance payment equal to 2.99 times his average annual compensation (includable in gross income for federal tax purposes) over the five years prior to the change of control and an additional “gross-up” payment to compensate Mr. Ives for any excise tax payable on such severance payment, together with payment for all accrued and unused vacation and sick leave; and (iv) in the event of Mr. Ives’ death, Mr. Ives’ estate will receive one month’s base salary together with payment for all accrued and unused vacation and sick leave.

Messrs. Guthrie and Keogh and Ms. Lessard. The new Employment Agreements for each of Mr. Guthrie, Ms. Lessard and Mr. Keogh also provide for certain payments to the applicable executive in the following events of termination of employment: (i) the executive will continue to receive his or her base salary for 12 months following termination by the Company without “cause” (as defined in the agreements), except for termination without cause following a “change of control” (as defined in the agreements), together with payment for all accrued and unused paid time off; (ii) the executive will continue to receive his or her base salary for 12 months following termination for “good reason” (as defined in the agreements), except for termination for good reason following a change in control, together with payment for all accrued and used paid time off; (iii) following a change of control, the term of the executive’s agreement will automatically be extended for two additional years, and if during the term of the agreement (as extended) his or her employment is terminated without cause or he or she resigns for good reason, the

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executive will receive a lump-sum payment equal to 18 months’ base salary then in effect (or, if greater, in effect immediately prior to the change of control), together with payment for all accrued and unused paid time off; and (iv) in the event of the executive’s death, his or her estate will receive one month’s base salary together with payment for all accrued and unused paid time off.

Employee Compensation Plans

Equity Incentive Plans.

The Company maintains the Heritage Bankshares, Inc. 1987 Stock Option Plan and the Heritage Bankshares, Inc. 1999 Stock Option Plan (collectively, the “Legacy Stock Option Plans”) for the benefit of key employees and nonemployee directors. Of the 480,000 shares authorized for option grants under the Legacy Stock Option Plans, 440,000 shares were authorized for grants to employees and 40,000 shares were authorized for grants to nonemployee directors. Concurrently with its approval of the 2006 Incentive Plan (described below), the Board of Directors terminated the Company’s ability to issue new awards under the Legacy Stock Option Plans.

In 2006 the Company adopted the Heritage 2006 Equity Incentive Plan, as amended and restated effective January 28, 2009, and subsequently amended January 25, 2012 and August 22, 2012 (the “2006 Incentive Plan”), which authorizes the grant of stock options, stock appreciation rights, restricted stock and certain other equity awards with respect to the Company’s common stock to key employees and non-employee directors. The maximum number of shares of the Company’s common stock that may be issued under the 2006 Incentive Plan is 250,000. The option price of either a nonstatutory stock option or an incentive stock option granted under the 2006 Incentive Plan will be the fair market value of the Company’s common stock on the date of grant. The Board of Directors recently amended the definition of “Fair Market Value” under the Plan to consist of the following: (i) the price of the last sale of a share of the Company’s common stock on the OTC Markets Group (or successor interdealer quotation system) occurring prior to the grant date of the applicable award; or (ii) if (i) is inapplicable, the fair market value as determined in good faith by the Board of Directors.

Deferred Compensation Plans.

Director Deferred Compensation Arrangement. In 1985, the Company entered into a deferred compensation and retirement arrangement with certain directors and subsequently with one officer. (As described below under “Director Compensation”, only one current director of the Company, Stephen A. Johnsen, is a participant in this deferred compensation plan.) The Company’s policy is to accrue the present value of estimated amounts to be paid under the contracts over the required service period to the date the participant is fully eligible to receive the benefit.

SERP. Under a Supplemental Executive Retirement Plan dated September 23, 2009 (the “SERP”), the Company will pay Michael S. Ives, our President & Chief Executive Officer, a total of $25,000 each year for ten years, in equal monthly installments (i.e., $2,083.33), beginning (i) the later of the first day of the month following (x) the day Mr. Ives’ employment with the Company ceases or (y) the day Mr. Ives attains the age of 67, or (ii) if Mr. Ives’ employment ceases due to his death or if the Board of Directors of the Company determines that Mr. Ives is disabled, on the first day of the month following death or disability; provided, if Mr. Ives’ employment with the Company ceases within two years following a change of control of the Company, then on the first day of the month following such separation from employment Mr. Ives will receive a lump sum payment equal to the present value of all installments of the $25,000 benefit amount to which Mr. Ives would otherwise be entitled. No benefits will be paid to Mr. Ives if his employment with the Company is terminated for “cause”.

Executive Deferred Compensation Arrangement. Pursuant to an Executive Deferred Compensation Agreement effective February 1, 2010, Mr. Ives may (but is not obligated to) elect to defer a portion of his annual base salary each calendar year (an “Elective Deferral”), pursuant to an advance election process that complies with Internal Revenue Code Section 409A. The Elective Deferrals and related investment earnings are nominally funded through a grantor Deferred Compensation Plan Trust (i.e., a “Rabbi Trust”), where the Company is the grantor for income tax purposes and pursuant to which assets of the Company are maintained as reserves against the Company’s obligations under the Executive Deferred Compensation Agreement. The Elective Deferrals are 100% vested at all times, and the Elective Deferrals and any related investment earnings are payable (in a lump sum and/or installments) at separation from service, a change in control of the Company, a specified date, or upon death and/or disability, as specified by Mr. Ives with respect to each Elective Deferral.

At December 31, 2012 and 2011, the Company’s other liabilities included a total of $1,060,000 and $1,009,000, respectively, related to these deferred compensation plans. In addition, compensation expense related to these plans was $77,000 and $82,000 (including approximately $21,000 and $20,000 in expense incurred by the Company in respect of the SERP maintained for Mr. Ives, as reflected above in the “Summary Compensation Table”) for the years ended December 31, 2012 and 2011, respectively.

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Other Employee Benefit Plans.

401k Retirement Program. Effective January 1, 1993, the Board of Directors adopted a 401(k) Retirement Program (the “401K Plan”). Eligible employees who have completed the required months of service are eligible to participate in and make contributions to the 401K Plan. The Company makes employer matching contributions. The Company expensed $98,000 and $99,000 for the years ended December 31, 2012 and 2011, respectively, in respect of the 401K Plan.

Employee Stock Bonus Plan. The Board of Directors adopted a stock bonus plan (the “ESOP”) effective January 1, 1998. The ESOP covered substantially all employees after they met eligibility requirements, and funds contributed to the ESOP were used to purchase outstanding common stock of the Company. The Company last made a contribution to the ESOP for the year ended December 31, 2005, and as a result no employees became entitled to allocations of ESOP contributions after that date. During 2011, the Board of Directors adopted resolutions terminating the ESOP, effective as of November 1, 2011. The Company has obtained approval from the Internal Revenue Service for termination of the ESOP, including the distribution of all remaining account balances to participants and beneficiaries entitled to them.

The Company recognized no compensation expense related to the ESOP for the years ended December 31, 2012 or 2011. Dividends received by the ESOP are used for administrative expenses of the plan. At December 31, 2012 and 2011, the ESOP owned 7,244 shares and 8,170 shares, respectively, of common stock of the Company. There were no contributions to the ESOP in the years ended December 31, 2012 or 2011. A total of 346 shares were purchased by the ESOP during 2012 and a total of 1,272 shares and 5,516 shares were distributed from the ESOP to terminated employees during 2012 and 2011. At December 31, 2012 and 2011, the fair market value of the shares held by the ESOP totaled $85,000 and $91,000, respectively.

Director Compensation

The table below presents information related to the compensation of the Company’s nonemployee directors (i.e., excluding Michael S. Ives, our President & Chief Executive Officer, who also serves as a director) for the fiscal year ended December 31, 2012.

Director Compensation for the Fiscal Year Ended December 31, 2012

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Director Compensation for the Fiscal Year Ended December 31, 2012

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(a) (1) Financial Statements. The financial statements for the Company are included under Item 8, “Financial Statements and Supplementary Data,” of the 2012 Annual Report on Form 10-K.

(a) (2) Financial Statement Schedules. All financial statement schedules required under Regulation S-X are omitted because they are inapplicable or because the required information is shown in the financial statements or the notes thereto.

(a) (3) Exhibits. The exhibits required by Item 601 of Regulation S-K are listed below.

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SIGNATURES

In accordance with Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has caused this Report to be signed on its behalf by the undersigned, thereunto duly authorized.

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