Payroll for Churches: Top 7 Payroll Software for Churches

Running church payroll in the modern day calls for dedicated software. Whether you need help creating a payroll plan, entering employee information, or handling workers’ compensation, payroll software for churches can handle it all. This article explores 7 of the best software options that offer unparalleled church payroll services. 

Table of Contents

FreshBooks

Gusto

MinistryWorks

SurePayroll

OnPay

QuickBooks Payroll

Rippling

Key Takeaways

Frequently Asked Questions 

FreshBooks

FreshBooks is the perfect accounting and payroll all-in-1 solution for small businesses and churches. The software program can quickly adapt to any business, including nonprofits and churches.

This comprehensive payroll program makes it a breeze to register contributions, customize invoices, compile financial reports, and much more.

The software program supports automated billing, bank reconciliation, ACH payment processing, and other features. FreshBooks breaks all the records when it comes to customer service. Zero hold time makes FreshBooks one of the best church payroll providers in terms of assistance.

The platform shares a large community and dedicated forums.. Plus, you’ll get help with tax calculations, tax laws, and any other issues you may have when running payroll.

Key Features

• All-in-1 accounting solution for churches
• Numerous app integrations
• Comprehensive workers’ compensation system
• Recurring payment scheduling
• Accounts payable
• Next-day direct deposit
• Tax automation
• Insightful reports

Pros

• Ease of use
• Excellent customer support
• Free trial
• Regular updates
• Affordability

Cons

• Not the best option for large organizations
• Limited mobile app

Gusto

Gusto is among the best church payroll service providers. Its full-service payroll system, affordable pricing, tax compliance assistance, and core HR features make it a reliable payroll management system. Gusto supports unlimited pay runs and automated taxes and forms.

All church workers receive access to the self-service portal to retrieve information about their pay online, and all employee information is encrypted.

Users can set tax exemptions for exempt employees, such as ministers. The software integrates with the nonprofit accounting software program Aplos, which tracks payroll automatically for nonprofit organizations and churches.

The main downside of the software is its lack of coverage for employee health insurance benefits. Some competitors on this list have benefits for all states, while Gusto only works in 39 of them. Overall, the intuitive dashboard and interface, ease of use, and efficient payroll tools make this a reliable church payroll service.

Key Features

• Efficient payment processing
• Tax payment and filing services
• Employee benefits
• Aplos integration
• Custom reports

Pros

• Automated and unlimited pay runs
• Online platform for employee self-onboarding
• Integration with Xero, QuickBooks, Aplos, and other third-party software

Cons

• Lack of dedicated personal payroll specialist
• Time tracking available only with higher tiers
• Health insurance benefits only for 39 states

MinistryWorks

MinistryWorks is one of the most popular church payroll services for ministries that need a separate payroll specialist only working with churches. This church payroll software is made for ministry and clergy tax law. It can run payroll, pay employees using direct deposits and checks, and handle federal, state, and local taxes.

Besides the Affordable Care Act (ACA) report feature, the software can manage tax withholdings and deductions. Plus, you get a dedicated payroll expert at your service.

Employee benefit features include pay-as-you-go employee compensation and a clergy housing allowance. MinistryWorks also includes health care reports, employee eligibility status tracking, and more.

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. MinistryWorks remains one of the most popular church payroll services on the market.

Key Features

• Robust payment processing
• Tax filings
• Tax penalty protection
• Employee benefits
• Payroll support experts

Pros

• Automated tax filing and payroll services
• Filing of state new hire reports
• A dedicated payroll professional

Cons

• Pay run fees
• Lack of benefit options
• Limited third-party integrations

SurePayroll

SurePayroll is excellent software for budget-friendly ministries. The platform offers flexible payroll solutions, including a full-service package. Administrators get access to automatic tax filings and payments and employee benefit plans.

SurePayroll features a payroll plan that excludes tax-filing services. 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.

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.

Key Features

• Payroll processing
• Employee benefits
• Plenty of third-party integrations

Pros

• DIY tax-filing features
• Automatic pay runs
• Reasonable pricing

Cons

• Additional cost for local tax filing for multiple states
• Extra cost for integrations

OnPay

OnPay is the best church payroll software for administrators who are looking for powerful system permissions to delegate HR and payroll tasks. This payroll software has 6 permission levels, so you can do payroll tasks and delegate HR and payroll tasks as you see fit.

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.

The strongest points of OnPay are its HR functionality, reporting tools, payroll features, and cost. Some downsides include a lack of third-party accounting and management software for churches. Also, consultations with HR advisors come at an additional cost. Still, most users appreciate the platform’s responsive customer support.

Key Features

• Unlimited payroll runs
• Basic HR tools
• Employee benefits
• Payroll tax filings and payments

Pros

• Unlimited payroll services
• Different payment options (manual checks, direct deposit, debit cards)
• Multiple-level system permissions for task delegation and payroll running

Cons

• No multiple tiers for varying HR needs and payroll functions
• No live phone support on weekends
• Limited integrations
• 2- and 4-day direct deposit depending on the platform’s risk assessment

QuickBooks Payroll

QuickBooks Payroll is the leading platform among churches that keep track of their bookkeeping. The combination of these 2 programs makes it easy to integrate payroll information across platforms.

The QuickBooks Payroll service offers some unique church-specific features. A good example is the multiple pay types for housing allowances. There are unlimited payroll runs, direct deposits to an employee’s bank account within a day, and more. The Premium plans support same-day payroll payments.

A minor disadvantage is the lack of a proper church payroll and tax expert service. Also, you must upgrade to the higher tier to access the local payroll tax-filing services.

You can expect to wait a bit longer to get a hold of a customer service representative at QuickBooks. Still, the platform remains user-friendly, and church payroll processing is a breeze.

Key Features

• Fast and efficient direct deposits
• Great payment processing
• Payroll tax filings
• Employee benefits
• Advanced payroll support
• Custom reports

Pros

• Limitless pay runs
• Same-day direct deposit
• Health benefits for all 50 states
• State new hire reporting

Cons

• Filing services and local taxes available only with higher plans
• Limited integrations
• Personal payroll specialists and HR advisors available only with higher plans
• State new hire reporting very limited

Rippling

Rippling is among the best church payroll services for churches that want to automate their payroll, IT, and HR tasks. Rippling allows users to automate core IT tasks like computer inventory monitoring, business software management, laptop assignment to personnel, and much more.

A comprehensive church payroll service like Rippling allows managers to focus on running the ministry and not spend hours on repetitive HR administrative processes. Payroll administrators can run payroll with 3 simple clicks. The system can automatically calculate wages and applicable tax deductions, create payroll forms, and file payrolls.

The platform is intuitive. However, many church-specific features can be a bit difficult to use. Also, the live support from the platform’s HR team is only available as a paid add-on. There are also no built-in payroll codes. Still, the system can handle tax exemptions for exempt employees.

Key Features

• Full-service payroll
• Integrated modular solutions
• Advanced HR tools
• Workforce automation software
• IT solutions

Pros

• Modular payroll, HR, and IT solutions with easy integration
• Compatibility with over 500 business apps
• Additional help for streamlining computer and app provisioning and de-provisioning

Cons

• Users must purchase basic workforce management to add other modules
• It’s not the most budget-friendly option
• Additional fees are charged for HR phone support

Key Takeaways

A proper church payroll system is a must for any church administrator who wants to make their job easier. The best church payroll software programs have all the features necessary to make payroll tax payments easier. Whether you’re new to payroll systems, want to upgrade your existing one, or need help with local tax payments, the solutions in this article can help.

FAQs on Church Payroll

Do Church Employees Pay Payroll Taxes?

Yes. All churches need to withhold income taxes from their employees’ wages. Clergy employees are different because of their dual tax status (SECA vs. FICA taxes).

Do Pastors Pay Payroll Taxes?

A church isn’t responsible for withholding taxes from a pastor’s salary. The responsibility for withholding taxes falls on the pastor. They must pay Social Security and Medicare by filing self-employment taxes.

Do Churches Have to Issue 1099s?

All organizations and businesses, including churches, need to file 1099s to inform the IRS about the income showing on the recipients’ income tax returns. The church is considered a reporting entity in this regard, much like any other business.

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