14 Best Church Payroll Software Reviewed For 2025

Deel is a global payroll and compliance platform that can be utilized by various organizations, including churches, to facilitate the hiring, onboarding, and payment of employees and contractors around the world. 

The platform offers tools for creating contracts compliant with local laws, processing payroll, and handling tax documentation, which can be particularly useful for churches with international missionaries or remote workers. Deel's ability to handle multiple currencies and payment methods, including cryptocurrencies, may also be beneficial for churches with diverse payment needs.

Deel integrates with multiple solutions, including Xero, BambooHR, Lever, Greenhouse, Workday, Quickbooks, Netsuite, Rippling, ADP, and Paychex.

OnPay is an online payroll service that offers solutions for payroll processing, HR, and benefits management. It aims to simplify these processes with features like automatic tax calculations, payroll setup, data migration, and integration with various business applications such as QuickBooks and Xero.

The platform simplifies the complex tax scenarios often faced by churches. For instance, OnPay automatically handles situations specific to clergy compensation and taxes, non-clergy members, and housing allowances. It also offers unlimited payroll runs.

Integrations include QuickBooks, Xero, Deputy, Guideline, Vestwell, Mineral, Magnify, and more.

Xero is an online accounting solution that doubles as a nonprofit accounting software. The platform has a beautiful build that’s easy to navigate and understand, so you should be able to find and use most of its features with minimal training.

The payroll tool helps you set up recurring pay runs and keep basic pay records. You can enter employee hours, set up and update hourly rates, and calculate deductions. You can send your staff payslips via email or you can print them. The platform stores the information online, so your church members can check their payslips using mobile devices.

Xero integrates with dozens of solutions, including EzzyBills, Stripe, Deel, HubSpot, Square, PayPal, and Zapier.

Gusto is a popular HR and payroll management solution. The platform is a great choice for modern churches because it enables you to set your employees up with benefits and manage paid time off. And the solution also creates an online database for your staff’s pay stubs, so they can check them out using mobile devices.

The great thing about using this app is that it files your taxes for you. Every time you run payroll, the solution files your tax sheets with the right federal or state agencies. The software keeps track of tax changes, so you don’t have to worry about misfilings.

Integrates with multiple apps, including Aplos church software, 15Five, 7Shifts, ActiveCampaign, Asana, Clover, QuickBooks, and Bonusly.

Wave is a cloud-based church software that allows you to check your accounting and financial information from wherever you are. The platform covers all the financial needs of a church, from payroll service to online donation processing and bank connections.

This software stands out thanks to its clean layout. Every feature and functionality is highlighted accordingly, so even people who are not tech-savvy can quickly learn their way around this tool.

The payroll feature allows you to generate W2 and 1099 forms in preparation for tax season and deposit money into your staff’s bank accounts. Wave also enables you to set up automated tax payments for specific states in the US.

Church Windows is a church management software with a good payroll feature. This solution creates a centralized location for all your accounting and financial information, so you can gain visibility into your finances and simplify your existing processes.

The highlight of using this platform to run payroll is that it allows you to generate checks, tax forms, reports, and allowances with ease. The Federal and State tax tables are updated when necessary, so you don’t need to change them yourself. You can also transfer your payroll information into the accounting module.

Church Windows has a slight learning curve, but the software’s support team can guide you through the payroll process.

Patriot Payroll is an online payroll service that offers an easy-to-use platform tailored for small organizations, including churches. It streamlines payroll management, providing a cost-effective and reliable solution for handling payroll processes efficiently. 

Patriot includes features essential for managing church payrolls, such as automatic tax calculations, direct deposit, and an employee portal for accessing pay stubs and W-2 forms. The full-service payroll option takes care of all federal, state, and local tax filings, ensuring compliance and reducing administrative burdens.

Additionally, its customizable pay rates and payroll reports allow for flexible and detailed management of church finances. Integrations include QuickBooks, TSheets, Gusto, Square, FreshBooks, and Xero.

CDM+ is an online church management software that enables clergy members to speed up their payroll process. The software creates an online portal for your employee so they can access their pay history, pay stubs, withholdings and deductions.

The solution also allows you to schedule direct deposits in advance, so you can automatically run payroll during bank holidays. The tool also helps you with other financial aspects, such as online giving tracking or fund accounting, and enables you to generate custom reports.

This software has a mobile-friendly version, so you can access it on any device, from anywhere, at any time.

PowerChurch Plus is an all-in-one church management software with dedicated payroll features. The solution helps you with church bookkeeping, financial management, as well as other aspects of church management.

This software creates a database for all your financial and personal records, making it easy to access information. You can also run payroll and pull reports on your contributions and accounts payable throughout the fiscal year.

The solution’s Knowledge Base helps you set up and maintain payroll according to federal and state laws. You can also access detailed guides and screenshots to speed up the setup process.

PowerChurch software integrates with several apps, including Vanco, Dynamic Systems, Avery, SimpleTexting, Clockify, and Constant Contact.

QuickBooks Payroll is a payroll management tool that assists businesses with automated tax calculations, filings, and time tracking. It stands out for its tax penalty protection feature, which safeguards businesses against potential tax penalties, positioning it as a reliable solution for tax compliance and protection.

I chose QuickBooks Payroll for church payroll software because of its comprehensive service offerings and user-friendly interface, which are particularly suited to the unique needs of church payroll management. What makes QuickBooks Payroll different is its automatic tax calculations and filings, which significantly reduce the risk of errors and penalties, a critical factor for non-profit entities like churches. I believe QuickBooks Payroll is best for tax penalty protection due to its robust compliance features and seamless integration with other QuickBooks products, catering to various business stages and industries.

QuickBooks Payroll integrates with 650 popular business apps including PayPal, Veem, Google Sheets, SaasAnt, Expensify, PaperEntry, BillBjorn, TimeSaver, ClockShark Time Tracking, Gusto, Run Powered by ADP, Guideline 401(k), Fundbox, Bill.com, and many others.