6 Best Church Payroll Services

Gusto scored better than the other providers because it offers a full-service payroll, tax compliance, and HR platform at an affordable price. It runs unlimited payroll, files federal and state taxes, including year-end reports, and pays employees through direct deposit or manual checks with no additional cost. Gusto also handles workers’ compensation, including employee health insurance and PTO policies. It provides church employees with access to their own portals where they can receive payday emails, lifetime accounts, and more.

Gusto supports church payroll needs by allowing you to set up tax exemptions for the church and its ministers. In addition, it integrates well with Aplos accounting that automatically tracks payroll and tax payments. Gusto also offers customer support and expert advice through phone, email, or live chat.

QuickBooks Payroll is best for churches who handle their own bookkeeping using QuickBooks Online to seamlessly integrate their payroll information. Its church-specific features, like multiple pay types for housing allowances, also make it a good option. It also offers unlimited payroll runs and you can send direct deposits to your employees’ bank accounts within 24 hours. With a Premium plan, you can even send payroll funds on the same day.

If you need to pay out a bonus or housing allowance immediately you can process it with no additional charge. Aside from helping you set up your payroll system (taxes, deductions, pay rates), QuickBooks Payroll calculates, pays, and files federal and state taxes and offers a tax-accuracy guarantee.

With Square Payroll, you are assured that you will have access to tools that will help you automatically process your payroll, calculate, and file your quarterly and annual taxes, and manage your employee benefits (health and workers’ compensation) anywhere. It also allows you to pay your employees by check, direct deposit, or cash app with no additional charge. Square Payroll has a mobile application that allows you to manage your team and run payroll anytime, plus it integrates with its Timecard app which makes paying hourly employees easy.

Square Payroll offers unlimited pay runs a month and integrates well with third-party providers like QuickBooks. You will also have live support during setup and can cancel anytime if you no longer need payroll services.

Patriot Payroll offers the most affordable online payroll application that allows churches to access their payroll from anywhere using a mobile phone. With Patriot Payroll, you can process unlimited pay runs and pay your church employees through direct deposit or manual checks. The Full-Service plan also files and pays all federal, state, and local taxes, regardless of location and offers a guarantee that your tax payments will be made on-time, or it will pay the penalties.

Patriot Payroll offers two flexible pricing plans: Basic and Full-Service. The Basic plan enables you to process payroll for 25 or fewer non-clergy employees that don’t require support for tax exemptions or housing allowances. But if you need both payroll and tax services, the Full-Service plan is the best option. Your employees can get access to an employee portal. Once you are signed up, you can have a free setup and expert support via phone, email, or chat.

MinistryWorks is a church payroll solution that specializes in clergy and ministry tax law and provides you with a dedicated payroll specialist. It runs payroll, pays your employees via checks or direct deposit, and handles all federal, state, and local taxes. It also manages tax withholdings and deductions in addition to new hire reporting.

In order to ensure that you are tax compliant, you’re also required to sign a limited power of attorney so MinistryWorks can represent you. In exchange, MinistryWorks will pay any fines that are a result of their errors.

It also integrates seamlessly with its in-house time-clock and you can always create a customized general ledger file at the department level. In addition, the software system can also handle multiple earnings, if your church employees perform more than one job, and deduction types.

Clergy Financial Resources is an all-inclusive church payroll software service that offers HR and clergy tax guidance. You can run an unlimited number of payrolls, calculate and pay both federal and state taxes electronically, and pay your employees using direct deposit or check with no additional cost. All tax calculations are also guaranteed to be accurate, or Clergy Financial Resources will pay for penalties and fees.

W-2 and 1099 reporting are also included. However, unlike Gusto, it doesn’t pay all local taxes (Pennsylvania or Ohio). Clergy Financial Resources gives you access to a dedicated clergy tax expert and a payroll specialist aside from the basic phone, chat, and email customer support. It also performs a church compensation and compliance review to ensure you are on the right track.