Although the colonial government had appointed auditors general from time to time, the office was not established on a permanent basis until after independence was declared. At its first session, which convened on 7 October 1776, the General Assembly passed an act creating a board of three auditors to examine and settle claims concerning receipts and expenditures for military purposes. The confusing financial situation of the state, however, resulted in a series of acts being passed over the next fifteen years elaborating and refining the duties of the auditors. Finally, at its session begun in November 1791, the General Assembly passed an act that combined the duties of the board of auditors and the solicitor general, whose office had been created in 1785 to settle the accounts of the state with the United States, and assigned them to a single auditor of public accounts effective 1 January 1792. The auditor soon became the most powerful fiscal officer in the state. All receipts and disbursements were made only upon his warrant to the treasurer, and his books were the standard against which those of the treasurer were checked.

The first changes were made as the accounts of the revolutionary era were settled. As the state moved into a period of steady financial and governmental growth in the nineteenth century, the number of accounts and funds maintained by the auditor became excessive. Thus, on 24 February 1823 the General Assembly passed an act creating the office of the second auditor to ease the auditor's burden. Although the second auditor handled several large special funds, the auditor continued to be responsible for most of the accounts concerning the daily operation of state government.

During the Civil War both the state government and the pro-Union Restored Government of Virginia, which was based first in Wheeling and then in Alexandria, had auditors of public accounts. After the war, near the end of Reconstruction, the military authorities appointed Major Thaddeus H. Stanton, of the United States Army, as auditor of public accounts. Stanton was paid by the state during his service from 3 April 1869 to 12 February 1870, although he remained an army officer. The position was returned to civilian control on 12 February 1870 with the election of William F. Taylor as auditor by the General Assembly.

Following the Civil War the complexities of an increasingly sophisticated financial world threatened to overwhelm the state fiscal offices, which had changed their practices but little since the end of the eighteenth century. Inadequate bookkeeping procedures and embezzlements of state funds resulted in a public demand for corrective action. It was not until a state government reorganization act was passed by the General Assembly on 18 April 1927, however, that the demand was satisfied. Effective 1 March 1928 the office of auditor of public accounts and second auditor were abolished and replaced by the office of comptroller--head of the Department of Accounts--to monitor the receipt and disbursement of state funds, and a new office of auditor of public accounts, under the General Assembly, to audit state and local government agencies.