18 Best Church Payroll Services Reviewed in 2025

Of course, our faith-based focus isn’t the only thing that sets us apart. We’re also dedicated to outstanding customer service when providing payroll for churches, and we will do whatever it takes to get the job done right the first time. When you work with ChurchShield, you are supported by our payroll team from day one of the onboarding process. Our team is also available during the payroll process to ensure that our clients have the information they need for their leadership best payroll service for churches teams. We understand the importance of managing time tracking, labor distribution reporting, and regulatory compliance.

Church payroll management

You’re looking at frustrated staff, possible tax issues, and (in the worst cases) legal trouble. That’s why finding the right church payroll service is so important. The right provider doesn’t just cut checks—it makes sure you’re compliant, organized, and stress-free. Aplos was built by a CPA and executive pastor, so they understand quite well that churches have unique accounting needs. That’s why Aplos church accounting software makes it simple for you to do accounting the right way.

Parable Church Accounting and Bookkeeping’s Financial Toolkit

Simplify Church Payroll is one of the most cost-effective solutions on the market today. SurePayroll can help you pay clergy, staff, and contract workers. This is just our site’s SEO section, created specifically for Google and our SEO team, and making it easier to connect with the best people on the planet (that’s you!). How to Invoice as a Freelancer Parable Church Accounting’s Financial Operating System brings you up-to-date.

• A minor disadvantage is the lack of a proper church payroll and tax expert service.
• FreshBooks’ award-winning customer support means you never struggle to get assistance.
• It manages all federal, state, and local tax filings, as well as running payroll and paying your workers through checks and direct deposits.
• We considered user reviews, including those of our competitors, based on a 5-star scale; any option with an average of 4+ stars is ideal.
• Wave is a cloud-based church software that allows you to check your accounting and financial information from wherever you are.
• Still, most users appreciate the platform’s responsive customer support.
• Track your financials and make informed decisions to grow your ministry.

Take the Stress Out of Filing Taxes

• We gave priority to church payroll services that have expertise in the unique tax treatment of clergy housing allowances and tax exemptions.
• With its Premium and Elite plans, you can even send payroll funds on the same day.
• With our longstanding expertise working with churches and ministries, we’re able to provide effective church payroll services that will correct previous mistakes and prevent these issues from continuing.
• If you’re looking for an integrated HR solution, be sure to take that into account as you research your options.

Features include time tracking and reports, budget building and estimates, customized quotes (so donors know the need), cost linking to jobs and projects, and reports that show how every donor dollar is spent. Whether you’re a multi-site mega-church with hundreds of employees or a small to medium-sized church with a handful of staff, you can find church payroll software that fits your needs. Software with standard payroll reports is considered robust, as well as those that are customizable and/or have functionality allowing users to build their own reports. Of the six providers we reviewed, only Payroll in QuickBooks, Gusto, and Square Payroll is a payroll service that allows you to pay offer employee portals with online onboarding. Gusto helps churches with payroll by enabling them to establish up tax exemptions for themselves and their preachers. It also works nicely with Aplos, a nonprofit fund accounting software that records payroll and tax payments for NGOs and churches automatically.

And unlike Gusto and Square Payroll is a payroll service that allows you to pay, it doesn’t integrate Certified Public Accountant with a lot of third-party software—you need QuickBooks Accounting to access its integration options. If not for the restricted coverage of its employee health benefits, it would have received better scores in our study. It also lacks a specialized payroll professional, like MinistryWorks, who can double-check your pay runs, as well as the services of a clergy tax expert, like Financial Resources for Clergy does. The best church payroll software doesn’t just “do payroll.” It handles complexity you shouldn’t have to think about—so your focus stays on ministry, not management. When you’re leading a church, the last thing you want is to be buried in admin work. If you’re stuck fixing tax errors or chasing pay stubs, you’re spending energy on the wrong things.