Few aspects of the tax code are as complicated and as opaque as the compensation offered to clergy and other church officials. All clergy were once classified as self-employed contractors — and, for the purposes of Medicare and Social Security taxes, they still are.
Clergy must pay the self-employment tax, or SECA, but they are considered employees. That is just the beginning of tax and payroll issues that must be addressed with church payroll software, like Advanced Micro Solutions’ 1099-etc software.
What Can Church Payroll Software Do?
A minister’s wages are exempt from income tax withholding, but some churches and religious members mistakenly believe that their tax-exempt status means that they do not need to file with the IRS/SSA at all. It can come as a rude awakening when the IRS does come calling.
Getting our church payroll software will provide you with:
- Both “live” and after-the-fact payroll calculations
- Forms filing tools
- Support for all 50 states, plus the District of Columbia and Puerto Rico
Catch up on your bookkeeping fast and stay caught up with AMS Payroll.
Church Payroll and Compensation Answered
Churches are under incredible pressure with uncertain information about how to pay their clergy in the first place. Some common questions include:
- How much does the senior pastor earn compared to the associate pastor?
- What about an administrative pastor who only fills in at the pulpit as needed?
Plus, all of this is before you get to other church officials, which will include the:
- Custodian
- Choir director
- Childcare provider
These people may command a salary or other forms of compensation. Many compensation types can be handled by our standard payroll features, but our system also includes 40 user defined fields that can be set up to handle more specialized church payroll software needs.
Discover a Better Software Solution with AMS
There is still actually doing the payroll and forms filing, even after your organization has figured out how to:
- Classify its clergy and church officials
- Constitute what is fair pay
Do not let the process become its own set of headaches. Find a versatile and affordable software solution with AMS.
It starts with the W-2/1099 Forms Filer, which is our intuitive, menu-driven platform and required system. Personalized data entry tools include an entry screen that resembles the actual form for clarity’s sake, as well as a spreadsheet format for church accountants who are looking to deliver that extra measure of efficiency with new church payroll software.
Tired of entering information more than once? You will never need to again with our:
- Automatic save feature
- Data importing
- Common Payee File feature
The platform offers the ability to print the information on pre-printed tax and payroll forms. If you use our Software Generated Forms module, you can even print out the forms themselves. Our Forms Filer provides information security, encrypted PDF files, and reliable data reports.
People Also Ask
- What is the best e-file software for churches? – Getting e-file software for churches should be affordable and comprehensive. Look for software that includes modular capabilities and easy formatting.
- What are the pitfalls in payroll software for nonprofit organizations? – It is important that you find software that simplifies your work rather than creating more of it. Make sure the software that you get includes time tracking, withholding capabilities, and supports all of your required forms.
Get Started with AMS Payroll
Our payroll module offers a huge range of features that can be leveraged by churches, as well as many businesses and other organizations. We encourage you to sign up for a free software demo, or speak with our Sales and Information team at (800) 536-1099.
Along with the software capabilities that we have already mentioned, here are some of the most popular features that are available with the software product.
- Automated federal, state, and local payroll tax calculations
- Direct deposit processing and paycheck printing (includes MICR checks with our Software Generated Forms module)
- Data import/export for quarterly and year-end filings
- E-file forms 940, 941, and/or 944
- Creates SSN verification files
- Certified payroll reports and client letter formatting
This article was updated on May 8, 2026 to keep its information as fresh as possible. We update this article every six months, before and after tax season, to keep current with any changes.