
The specialized ministry payroll feature ensures churches receive special exemption status when it comes to taxes and other related processes, making it easier than ever before to manage employee payments. On top of that, MinistryWorks also offers an audit assistance feature which gives churches the confidence they need when submitting payroll documents. At ChurchShield, our experts understand that payroll for churches can be complex, and we have found that almost 90% of clients who have us review their payroll for the first time have errors that need to be corrected. This is almost always because the processing is being done according to standard corporate laws as opposed to church laws.
If you do a quick search on Google, you will find a lot of different church payroll services, all offering to carry that burden. But, not all are created equal, and when dealing with tax compliance especially, you need to know what options are the best and wisest choice. Payroll is a very important aspect of every church, so choosing the best payroll services is imperative. Running payroll is not only about ensuring employees get compensated, but also about making sure their hours are accurate, staying compliant with clergy tax law and supporting you throughout the process.

The software integrates with the nonprofit accounting software program Aplos, which tracks payroll automatically for nonprofit organizations and churches. The software program supports automated billing, bank reconciliation, ACH payment processing, and other what are retained earnings features. Zero hold time makes FreshBooks one of the best church payroll providers in terms of assistance. If you want a simple payment plan for church payroll plus some HR features, then OnPay is an excellent choice.


They specialize in small to medium-sized organizations, so this payroll service is worth checking out if you’re a smaller church. Much like QuickBooks and Gusto, this software supports unlimited and automatic pay runs. It can help with salary calculation and deduction for employees and support church allowance payments. Besides the Affordable Care Act (ACA) report feature, Bookstime the software can manage tax withholdings and deductions.
Rippling allows users to automate core IT tasks like computer inventory monitoring, business software management, laptop assignment to personnel, and much more. All QuickBooks Payroll plans come with full-service payroll, automated taxes and forms, and next-day direct deposits. If you upgrade to higher tiers, you get additional features like time tracking and a tax penalty protection that covers filing errors that you or its representatives make.
Read our advice on how to pick a payroll service if you need assistance deciding which provider is best for your company. At ChurchShield, we strive to be a valuable asset for your church and want to help alleviate the stress that comes with ongoing payroll church payroll processing and compliance. That way, you can continue to do what you do best, which is address the needs of your congregation. And, if they do, does your church website make an outstanding first impression? At REACHRIGHT, we understand the unique challenges busy churches and ministries face when it comes to online marketing. And we know first-hand what it takes to create an effective digital marketing strategy for churches.
This plan is ideal for administrators who want to save money by submitting tax forms independently. The reporting features, HR functionality, and price make this one of the most flexible church payroll services. The overall user-friendly interface and stable customer service are 2 more reasons for its popularity.

With surepayroll’s intuitive interface and helpful customer service team, churches can rest assured that their payroll needs will be met quickly and efficiently. The importance of payroll services for ministries and clergy cannot be overstated. Many churches are now turning to payroll services to help them manage the unique financial resources given to their clergy. It’s a complex area, requiring a deep understanding of allowance versus salary payments and health plan access for ministers. To make sure your ministry is following best practices for church allowance payments and providing affordable health benefits to its clergy, enlisting the help of an experienced payroll service can be invaluable.
The system lets users choose solutions (online forms, PTO filings) that clergy or non-clergy employees can access. It also offers full-service payroll processing, unlimited pay runs, health insurance benefit access for all states, and more. You can even use OnPay to calculate clergy staff payments by excluding federal unemployment taxes. Compared to other solutions on this list, MinistryWorks has limited pay runs and doesn’t feature quick direct deposits. The platform lacks a report builder for custom reports, and users may find limited support for third-party integrations. Still, most users appreciate the ease of use and responsive payroll specialists.