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Church Payroll Guide

Church tax exempt status

Churches that meet the requirements of Section 501(c)(3), the federal law governing charitable tax exemptions, get church tax exempt status automatically and do not need to apply to the IRS. They also don't file the yearly return most charities do, though a few other forms and an IRS ID number still matter.

Does a church have to apply to be tax exempt?

No application is needed, provided it meets the Section 501(c)(3) rules. Churches that qualify are treated as tax exempt automatically and never need to send in an application.

To be eligible, a church must be set up and run solely for religious, educational, scientific or similar charitable ends (IRS Publication 1828). Donors may still deduct their gifts even when the church has never sought IRS recognition.

Do churches have to file Form 990?

Most tax-exempt organizations send the IRS a yearly return called Form 990 or 990-EZ. Churches and some church-affiliated organizations do not have to file Form 990 or 990-EZ.

Other charities automatically lose their exemption after missing 3 years of returns. Since a church has no annual return in the first place, this automatic revocation rule doesn't apply to churches.

A denomination's group ruling can cover some churches. The IRS updated those rules with Revenue Procedure 2026-8, issued in January 2026. Churches covered by a group ruling still do not file Form 990.

Churches and the 990-T: business income

A church may still have to file one return in the 990 family. A church must file Form 990-T if it receives $1,000 or more in gross income from an unrelated business during the year (IRS Publication 1828).

Form 990-T falls due on the 15th day of the fifth month once your church's tax year closes (IRS Publication 1828). If your church's year runs January to December, that date is May 15.

Getting an EIN for your church

An EIN is the ID number the IRS gives an organization. According to the IRS, each church should have one, even if it has no employees (IRS Publication 1828). Your church will use its EIN when opening a bank account and when filing Forms W-2, 1099 and 990-T.

A church that pays staff also puts the EIN on Form 941. That form is the quarterly federal tax return for reporting the income tax and FICA taxes a church withholds from employee pay (IRS Publication 1828).

You can request an EIN through the IRS website, or by mailing or faxing Form SS-4:

  1. Complete Form SS-4, or its online version, using your church's name and address.
  2. Select "church or church-controlled organization" for the entity type.
  3. Submit it over the internet, through the mail or via fax.

The IRS gives out EINs online at no cost, and no fee is ever required.

What puts a church's tax exemption in danger?

Even without ever applying, a church can lose its exemption over a few things:

  • Political campaigns. Churches may not join in any political campaign, whether for a candidate or against one (IRS Publication 1828), whether directly or indirectly. Breaking this rule can cost the exemption and bring an extra tax.
  • Overpaying insiders. Any amount of church funds that unfairly benefits insiders, like unreasonable pay, may be grounds for losing the exemption.
  • Too much lobbying. Limited lobbying is fine, but once lobbying becomes a substantial part of what your church does, the exemption is at risk.

Insiders who receive an excess benefit may personally owe taxes reaching as high as 225 percent of that benefit.

Questions churches often ask

Why apply for 501(c)(3) recognition when exemption is automatic?

Many churches apply anyway, since formal IRS recognition gives leaders, members and donors confidence in the church's exempt status and in the tax benefits attached to their gifts. The application is Form 1023, and it comes with a $600 user fee that you pay via Pay.gov at the time of filing.

May a church endorse a political candidate?

No, not at the moment. According to Holtzman Vogel's 2026 election-year guide, the Johnson Amendment still applies for the November 3, 2026 election. A church may still discuss issues, register voters and hold even-handed candidate forums, provided it never backs or opposes any particular candidate.

On March 31, 2026, a Texas federal court rejected an IRS settlement that would have allowed churches to endorse candidates from the pulpit. Then, in a filing dated September 21, 2026, the Justice Department urged the Fifth Circuit appeals court to bring the case back, so the matter remains unresolved.

Is our EIN also our state tax-exempt number?

No. The EIN isn't your church's state tax-exempt number.