After you give an IRS supervisor the chance to talk you out of appealing, you can officially file. Make sure you do so within 30 days of the official IRS determination.
The IRS Appeals Office will be the one considering your appeal. According to the IRS, the office is independent of the Exempt Organizations unit and other IRS divisions, so you don’t have to worry about any preconceived bias.
If you are unable to settle your claim with the Appeals Office, you have the right to petition the U.S. Tax Court, the U.S. Court of Federal Claims or the U.S. District Court for the District of Columbia concerning your organization’s 501(c)(3) status. If you get a favorable judgment at this level, the IRS has to follow it.
Contact your legal professional for further advice about appealing an IRS decision. Remember that if you don’t appeal now, you won’t be able to seek relief in court later.