The Accounting Office is responsible for the State System's consolidated financial audit and single (A-133) audit, System-wide accounting policies and procedures, and the financial management of the Office of the Chancellor. The Accounting Office provides leadership in the development and maintenance of the financial modules of the Shared Administrative System. In addition, the Accounting Office is responsible for the finance section of the annual Integrated Postsecondary Educational Data System (IPEDS), the Board of Governors Travel Regulations, and all other accounting-related issues.

The Payroll Accounting Office is responsible for filing the required federal, state, and local payroll tax returns for the System, as well as for the reporting and payment of all other amounts withheld from employees, such as retirement and health benefits.