Like any other organization, churches and ministries need to process their payroll and comply with IRS tax rules. Aside from managing pay processing and tax withholdings and filings at an affordable rate, the best church payroll services offer features like church-specific tax law expertise that make running payroll easier.
In this guide, we evaluated 15 providers to find the best church payroll services and narrowed it down to our top six.
- Gusto: Best overall church payroll service for solid hiring and HR tools
- SurePayroll by Paychex: Best for small churches wanting budget-friendly payroll plans with full-service and do-it-yourself (DIY) tax filings options
- OnPay: Best for those needing setup support and robust system permissions to delegate payroll tasks
- QuickBooks Payroll: Best for churches that want fast direct deposits and low-cost contractor payments
- Rippling: Best for tech-savvy churches looking for customizable workflows to automate payroll, HR, and IT tasks
- MinistryWorks: Best for ministries requiring a dedicated payroll specialist that only works with churches
QuickBooks Payroll is a great option for businesses that have many different types of employees due to its versatility, ease of use, and wide variety of features. |
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Top Church Payroll Services Compared
All the church payroll software on our list offer full-service payroll, tax filing services, W-2 and 1099 tax forms at year-end, and unlimited pay runs (except MinistryWorks). Below are some of the features and pricing details of each provider.
Quiz: Determine the Ideal Church Payroll Software for You
Unsure which church payroll service to get? This quiz will help you decide.
If you still need help selecting a provider that’s right for you, read our guide on how to choose a payroll service. Meanwhile, check our guide to the best church accounting software to help improve transparency, efficiency, and financial management of church funds.
Gusto: Best Overall Payroll Software for Churches
Pros
- Unlimited and automated pay runs; also supports international contractor payments
- Online portals for employee self-onboarding
- Integrates with several third-party software (like Aplos, Xero, Clover, and QuickBooks)
- HR tools include job postings, applicant tracking, and employee performance reviews
Cons
- No dedicated payroll specialist
- Health benefits coverage limited to 39 states
- Time tracking, multistate payroll, and advanced HR tools are included only in higher tiers
Gusto is the best payroll service for churches because it offers solid pay processing with tax compliance and HR tools at a reasonable price. It supports church payroll needs by allowing tax exemptions for the church and ministers. Church employees can also access their pay information through a self-service portal. It even integrates well with Aplos, a nonprofit fund accounting software that tracks payroll and tax payments for nonprofits and churches.
If you need to hire new staff, Gusto offers the essential tools for posting job openings, managing applicants, and scheduling interviews. Online offer letter templates are available once you’ve selected a qualified candidate to hire. You can also start the onboarding process, allowing your new employee to complete new hire paperwork and requirements online.
In our evaluation, Gusto earned an overall rating of 4.34 out of 5. It would have gotten higher scores had it not been for the limited coverage of its employee health benefits. Compared to providers like OnPay and SurePayroll by Paychex, which have benefits available in all US states, Gusto’s health insurance options are limited to only 39 states as of this writing. It also doesn’t have a dedicated payroll specialist who can help double-check your pay runs, something MinistryWorks offers.
Gusto Overview
SurePayroll by Paychex: Best for Small Churches Looking for Budget-friendly Payroll Plans
Pros
- Flexible payroll plans with a DIY tax filing option
- Unlimited and automatic pay runs
- Affordably priced
Cons
- Charges add-on fees for multiple state and Ohio/Pennsylvania local tax filings
- Software integrations cost extra; with limited options (doesn’t connect with church management systems)
This provider’s payroll services for small churches make it a good option for those looking for budget-friendly and flexible pay processing options. It offers a full-service payroll package (costing $29.99 plus $5 per employee monthly) with access to employee benefits plans and automatic tax payments and filings. SurePayroll by Paychex also has a payroll plan that doesn’t include tax filing services (priced at $19.99 plus $4 per employee monthly)—ideal for those who prefer to save money remitting tax payments and submitting tax forms themselves.
SurePayroll by Paychex earned an overall score of 4.16 out of 5 in our evaluation. Its transparent pricing, affordability, and reporting capabilities contributed to its high rating. While it has user-friendly and efficient payroll tools, its church-specific functionalities aren’t as robust as MinistryWorks, which offers church payroll advisers who can offer expert advice. Its platform also doesn’t connect with church management systems as Gusto does, and some of its time tracking and accounting integrations cost extra.
SurePayroll by Paychex Overview
OnPay: Best for Setup Support and Robust System Permissions to Delegate Payroll Tasks
Pros
- Unlimited payroll
- Multiple payment options (like direct deposits, manual checks, and debit cards)
- Six-level system permissions allow you to delegate tasks and run payroll however you want
- New clients get free account migration and integration setup
Cons
- Lacks multiple tiers that cater to varying payroll and HR needs
- Doesn’t have live phone support during weekends (only email)
- Limited third-party software integrations
- Eligibility to two- or four-day direct deposits depend on OnPay’s risk assessment
New clients transitioning to OnPay won’t have to worry about system setup and data migration because the provider will handle this for them. The service also includes setting up and customizing time tracking and accounting integrations you might need (the others on our list either charge extra for this or only offer it in higher tiers). Plus, its six levels of system permissions allow you to delegate payroll tasks, as well as select the solutions (such as online forms and PTO filings) that your clergy and non-clergy employees have access to.
Its full-service payroll, unlimited pay runs, and access to health benefits across all US states contributed to its overall rating of 3.98 out of 5. It would have ranked higher on our list if its church-specific tools included integrations with church management software. While it provides access to HR advisers through its partner, Mineral HR, you have to pay extra for it ($20 monthly for contacting an HR expert).
OnPay Overview
QuickBooks Payroll: Best for Churches That Want Fast Direct Deposits & Low-cost Contractor Payments
Pros
- Unlimited pay runs
- Next- and same-day direct deposits
- Seamless integration with QuickBooks Accounting
- Low-cost contractor payments plan
- Robust tax penalty protection
Cons
- Time tracking, local tax payment and filing services, and HR advisory services are included in higher tiers
- Limited third-party integrations; you need QuickBooks Accounting to access all options
- Health plans aren’t available in Hawaii, Vermont, and the District of Columbia (as of this writing)
QuickBooks Payroll is perfect for those looking for church payroll services that integrate seamlessly with QuickBooks Online. This makes handling church accounting and pay processing easy for ministries. Plus, its fast direct deposits, affordable contractor plan, and multiple pay types that support clergy-related allowances also make it a good option for churches.
While all QuickBooks Payroll plans come with full-service payroll, automated taxes and forms, and next-day direct deposits, upgrading to its higher tiers will unlock additional features like time tracking and a tax penalty protection that covers filing errors that you or its representatives make. These functionalities contributed to the provider’s overall score of 3.93 out of 5. However, its rating was pulled down by its limited third-party software integrations and the lack of in-house church payroll and tax experts (which MinistryWorks has).
QuickBooks Payroll Overview
Rippling: Best for Tech-savvy Churches Wanting to Automate Payroll, HR & IT
Pros
- Modular HR, payroll, and IT solutions integrate seamlessly (you can choose features that your organization needs)
- Connects with 500+ business apps
- IT tools help streamline computer/app provisioning and deprovisioning processes
- Offers global payroll and hiring, including professional employer organization (PEO) services for outsourcing HR administration tasks
Cons
- Its core workforce management solution must be purchased before adding other modules
- Gets pricey as you add features
- HR advisory services cost extra
- Lacks live phone support (but you can request a call through its live chat)
What makes Rippling a good option for churches is its all-in-one solution that not only streamlines HR and payroll processes but also automates basic IT tasks—from monitoring computer inventory to managing business software and assigning laptops to personnel. This allows you to focus more on running your ministry and less on handling day-to-day HR administrative processes.
Rippling scored 3.73 out of 5 in our evaluation given its intuitive and feature-rich platform, solid payroll and HR tools, and reporting functionalities. However, it lost several points because live phone support from HR advisers is a paid add-on and it lacks built-in special church payroll codes (although it can handle tax exemptions for clergy employee payments). It also doesn’t assign dedicated church payroll specialists to its clients like MinistryWorks does.
Rippling Overview
MinistryWorks: Best for Ministries Needing a Dedicated Church Payroll Specialist
Pros
- Automated payroll and tax filings
- Files state new hire reports
- Access to a dedicated payroll specialist
Cons
- Charges per pay run; can get pricey depending on your pay frequency and the number of employees you have
- Limited benefits options
- Very few third-party software integrations
- HR solutions are paid add-ons
MinistryWorks is a church payroll software specializing in clergy and ministry tax law. It runs payroll, pays your employees via checks and direct deposits, and handles all federal, state, and local tax filings. In addition to Affordable Care Act (ACA) reporting, it manages tax withholdings and deductions and even provides you with a dedicated payroll specialist that can help manage pay runs.
Overall, it earned a score of 3.69 out of 5 in our evaluation. While it has dedicated payroll support, robust church pay processing features, and a generally easy-to-use platform, its limited integration options, per-pay run charges, and add-on fees for basic HR tools (like time tracking and onboarding) cost it several points.
MinistryWorks Overview
Looking for a wider range of payroll options? Check out our buyer’s guides on the best payroll services and best payroll software.
How We Evaluated the Top Church Payroll Services
We compared 15 payroll services for small churches, looking for functionalities we believe are most important for ministries. These features include payroll and tax management tools specific to church payroll, plus attributes that make the service easy to use. We also considered providers that offer affordable pricing options, church payroll support, multiple payment options, and basic HR solutions for managing onboarding and employee benefits.
Click through the tabs in the box below to view our full evaluation criteria.
25% of Overall Score
We gave priority to those that offer automatic payroll runs and multiple payment options with at least a two-day direct deposit option. We also looked for tax payment and filing services that cover all levels (federal, state, and local taxes), including year-end tax reporting (W-2s and 1099s).
20% of Overall Score
We looked at the monthly payroll costs, including set-up and year-end fees. Preference was given to providers that have unlimited pay runs and starter payroll plans that cost less than $50 per month for one employee.
20% of Overall Score
We checked if the payroll service and solution are easy to use and have intuitive features. Additional points were given to providers who offer live phone support and can handle most of the client’s pay processing needs. We also considered integration options and user review ratings from popular third-party review sites (like G2 and Capterra).
20% of Overall Score
We gave priority to church payroll services that have expertise in the unique tax treatment of clergy housing allowances and tax exemptions. We also looked into providers that integrate well with existing church management systems and accounting software.
10% of Overall Score
We looked for basic HR tools, such as online onboarding, state new hire reporting, employee benefits options, and a self-service portal that workers can use to see payments made, edit information, and/or print forms.
5% of Overall Score
Preference was given to software with built-in basic payroll reports and customization options.
How to Choose the Best Church Payroll Software
In selecting the right church payroll service for your ministry, consider the following factors:
- Cost: Compare the fees charged by different providers and assess whether they offer a good balance between cost and the services offered.
- HR payroll features: Take stock of the features that you need. Consider providers that offer direct deposit payouts, time tracking, and employee self-service portals. For payroll compliance, you should assess whether the provider understands the unique needs and regulations related to churches and ministries. Ensure that the provider has a solid understanding of payroll tax rates, and if it handles tax withholdings, filings, and reporting accurately and in a timely manner.
- Integration with other systems: If you use accounting or church management solutions, check whether the payroll software can integrate smoothly with those systems. Compatibility and seamless data transfer can save time and reduce errors.
- Ease of use: Look for church payroll software that is easy to set up, learn, and use. You should also check the workflow automation options offered as these will help streamline HR and payroll processes.
- Customer support: Prompt assistance and guidance, including access to live support, are essential in case of any issues or questions that may arise. Make sure to look at user reviews and testimonials to gain insights into its reliability, customer service, and overall satisfaction levels.
Frequently Asked Questions (FAQs)
Anyone who is an employee of the church and receives a regular salary should be on the church payroll. This includes pastors, administrative staff, and other church employees.
Church employees who have non-clergy roles are required to pay payroll taxes, such as Social Security, Medicare, federal, state, and local taxes. Churches are also required to withhold and pay these taxes on behalf of their employees. Meanwhile, clergy staff members (like priests and ministers) are exempt from Social Security and Medicare taxes.
Church employees typically receive a W2 form at the end of the year, which reports their wages and taxes withheld. However, if an employee is considered an independent contractor, they may receive a 1099 form instead. It is important for churches to properly classify their workers as employees or independent contractors to ensure compliance with tax laws and regulations.
Bottom Line
Churches and ministries have more complicated requirements than general small businesses and need access to clergy tax law and church payroll practice expertise. Depending on your budget, there are different church payroll services to choose from. Apart from affordability, the best church payroll services should have features that help ministries pay clergy and non-clergy employees efficiently and, at the same time, be tax compliant.
We found that Gusto offers all of the features churches would need to facilitate their payroll and tax compliance needs. It’s easy to use and handles tax filings for you, and the price is reasonable when compared to other church payroll services. Sign up for a Gusto plan today.