A payroll tax audit is an examination by the IRS or the California Employment Development Department of whether you have correctly withheld, reported, and paid payroll taxes on behalf of your employees. The IRS runs its own audit under the Federal Insurance Contributions Act (FICA) and the Federal Unemployment Tax Act (FUTA) — 941s and 940s. The EDD runs a separate audit under California Unemployment Insurance Code. Both can happen at the same time, and they often do.
The mechanics are different depending on who is auditing you. An IRS employment tax exam will typically focus on three things: whether you calculated withholding correctly, whether you deposited on time, and whether you properly classified workers. The EDD audit covers similar ground under California law, plus UI, SDI, ETT, and PIT withholding. Both agencies have the authority to assess back taxes, penalties, and interest — and the IRS can assess the trust fund recovery penalty personally against whoever was responsible for collecting and paying over those taxes. That personal liability does not go away in bankruptcy.
Worker classification is where most payroll tax audits become serious. If you treated someone as an independent contractor and the agency decides that person was actually your employee, you owe the employer’s share of FICA, plus the employee’s share you failed to withhold, plus failure-to-file and failure-to-pay penalties. California uses the ABC test under AB5, which starts from a presumption of employment. It is one of the strictest classification standards in the country. The IRS uses a common-law test that weighs behavioral control, financial control, and the nature of the relationship — but “we paid them on a 1099” is not a defense on its own.
The trust fund recovery penalty deserves its own mention. Under IRC § 6672, the IRS can assess the unpaid employee portion of FICA directly against any “responsible person” — an officer, a member-manager, a bookkeeper, anyone who had the authority to direct that the taxes be paid and chose not to. The penalty equals 100% of the unpaid trust fund taxes. The IRS does not need to collect from the business first. If you are a company officer or a majority owner, you should assume you are a responsible person until shown otherwise.
Getting ahead of a payroll tax audit matters. Auditors set the scope of the exam in the opening stages. Responses you give before retaining representation become part of the record. If you received an audit notice from the EDD or an IDR from the IRS payroll division, the right move is to get representation in place before you respond — not after. We have handled payroll tax audits at both the IRS and EDD level, and we know where the issues typically arise and where they do not.
If you are dealing with an EDD audit or an IRS employment tax exam, book a free 15-minute call or call us at (619) 378-3138.