6 Best Church Payroll Services for 2022

Like any other organization, churches and ministries need to process their payroll and comply with IRS tax rules. Aside from managing the usual pay processing and tax withholdings and filings at an affordable rate, the best church payroll services offer features such as church-specific tax law expertise that make running payroll easier.

We evaluated 13 providers to find the best church payroll services and narrowed it down to our top six.

• Gusto: Best overall church payroll service
• QuickBooks Payroll: Best for church QuickBooks users and churches that want fast direct deposit options
• Patriot Payroll: Best for churches that want flexible payroll plans with budget-friendly do-it-yourself (DIY) tax filings and full-service options
• MinistryWorks: Best for ministries that need a dedicated payroll specialist
• Square Payroll: Best for ministries looking for a way to send paychecks instantly without paying extra
• Clergy Financial Resources: Best for churches that need HR and payroll compliance help

Top Church Payroll Services Compared

If you need help choosing a provider that’s right for your business, read our guide on how to choose a payroll service.

Gusto: Best Overall Church Payroll Service

Gusto

Overall Score: 4.18 OUT OF 5

RATING CRITERIA	Church-specific Features	2.00	OUT OF	5
	Ease of Use	3.88	OUT OF	5
	HR Features	4.00	OUT OF	5
	Payroll Features	4.75	OUT OF	5
	Pricing	5.00	OUT OF	5
	Popularity	5.00	OUT OF	5
	Reporting	5.00	OUT OF	5

What We Like

• Unlimited and automated pay runs
• Online portals for employee self-onboarding
• Integrates with several third-party software (like Aplos, Xero, Clover, and QuickBooks)

What's Missing

• No dedicated payroll specialist
• Health benefits coverage limited to 39 states
• Time tracking included only in higher tiers

Gusto Pricing

• Core: $39 per month + $6 per employee monthly
• Complete: $39 per month + $12 per employee monthly
• Concierge: $149 per month + $12 per employee monthly
• Contractor-only plan: $6 per contractor monthly

Gusto scored better than the other providers because it offers full-service payroll, tax compliance, and basic HR tools at an affordable price. It offers unlimited pay runs, automated taxes and forms, and state new hire reporting. Church employees are also granted access to a self-service portal where they can access and view pay information online.

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, a nonprofit fund accounting software that automatically tracks payroll and tax payments for nonprofits and churches.

Overall, it earned a score of 4.18 out of 5. It would have gotten higher ratings in our evaluation had it not been for the limited coverage of its employee health benefits. Compared to providers like QuickBooks Payroll and Square Payroll in which benefits are available in all US states, the coverage of Gusto’s health insurance options is 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 like MinistryWorks provides or the services of a clergy tax expert that Clergy Financial Resources offers.

However, many users still raved about its ease of use, intuitive interface, and efficient payroll tools. Some, on the other hand, said that while it generally provides good customer service, contacting its support team can be a bit difficult at times.

Gusto Features

• Efficient pay processing: In addition to automatic and unlimited pay runs, you can pay church employees via manual checks and direct deposits (two- and four-day options). It also offers next-day direct deposits—provided you subscribe to its higher tiers. But if you require faster direct deposits, QuickBooks Payroll is a great alternative as it has a same-day option.
• Tax payment and filing services: Depositing and filing payroll taxes won’t be a problem since Gusto handles that for you. Given that ministers may be exempt from certain taxes (like Medicare and Social Security), you can set up a church-specific tax exemption directly in the system. This is unlike Square Payroll and Patriot Payroll, which don’t have built-in special codes for church payroll.
• Employee benefits: With Gusto, you get a wide range of benefits options—health insurance, dental and vision, 401(k) plans, workers’ compensation, and a health reimbursement program. MinistryWorks, Square Payroll, Clergy Financial Resources, and QuickBooks Payroll may offer benefits but the selection isn’t as robust. However, Gusto’s health insurance plans are not available in 11 states (Alabama, Alaska, Hawaii, Louisiana, Mississippi, Montana, Nebraska, North Dakota, South Dakota, West Virginia, and Wyoming). If your business is in one of these states, then consider QuickBooks Payroll or Square Payroll. Patriot Payroll doesn’t offer benefit options for employees.
• Clergy housing allowance: Setting up a housing allowance for ministers and the clergy is easy with Gusto. You can even add the allowance amount as a recurring reimbursement.
• Integration with Aplos: Gusto is the only church payroll software that we reviewed that connects seamlessly with Aplos, making it easy for you to track payroll and tax payments. It also integrates with several third-party solutions like QuickBooks, Xero, Homebase, and When I Work.
• Custom reports: Aside from customizable reports, Gusto offers an online report builder that allows you to create your own reports directly from its system. Of the six church payroll services we reviewed, only Gusto and QuickBooks Payroll have this feature.

Read Our Gusto Review

QuickBooks Payroll: Best for Church QuickBooks Users & Churches Wanting Fast Direct Deposits

QuickBooks Payroll

Overall Score: 4.01 OUT OF 5

RATING CRITERIA	Church-specific Features	3.00	OUT OF	5
	Ease of Use	4.00	OUT OF	5
	HR Features	4.38	OUT OF	5
	Payroll Features	4.13	OUT OF	5
	Pricing	5.00	OUT OF	5
	Popularity	2.50	OUT OF	5
	Reporting	5.00	OUT OF	5

What We Like

• Unlimited pay runs
• Next- and same-day direct deposits
• Health benefits cover all 50 US states

What's Missing

• Local tax payment and filing services available only in higher tiers
• Limited third-party integrations (mostly integrates with QuickBooks products); you need QuickBooks Accounting to integrate with other software
• Access to a personal HR adviser and 24/7 payroll support experts only included in its highest tier

QuickBooks Payroll Pricing

• Core: $45 per month + $4 per employee monthly
• Premium: $75 per month + $8 per employee monthly
• Elite: $125 per month + $10 per employee monthly

QuickBooks Payroll is best for churches that 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 offers unlimited payroll runs and you can send direct deposits to your employees’ bank accounts within 24 hours. With its Premium and Elite plans, you can even send payroll funds on the same day.

While QuickBooks Payroll earned an overall score of 4.01 out of 5 in our evaluation, its rating was pulled down by a lack of in-house church tax experts (which Clergy Financial Resources has) and the need to upgrade to its higher tiers for local payroll tax filing services. And unlike Gusto and Square Payroll, it doesn’t integrate with a lot of third-party software—you need QuickBooks Accounting to access its integration options.

Many user reviews said it has a user-friendly platform that helps make pay processing easy. However, some users commented that while its customer representatives are helpful, the time it takes before they can chat or speak with someone is a bit long at times.

QuickBooks Payroll Features

• Fast direct deposits: Unlike the other church payroll services we reviewed in this guide, QuickBooks Payroll offers same-day direct deposits in addition to a next-day option (which is its standard direct deposit turnaround time). You do have to subscribe to its Premium or Elite plan to gain access to same-day payouts.
• Efficient pay processing: QuickBooks Payroll provides automatic and unlimited pay runs at no extra cost. This is unlike MinistryWorks where you are charged for each payroll run. It lets you set up church-specific tax exemptions and clergy housing allowances, and pays employees via direct deposits and paychecks.
• Payroll tax filings: QuickBooks can handle payroll tax calculations and filings for federal and state, including end-of-year reports. While it calculates local taxes, it doesn’t file local tax forms unless you subscribe to its higher tiers. Of the six church payroll services we reviewed, only QuickBooks Payroll doesn’t include tax filings for all levels in its starter tier.
• Employee benefits: Unlike Gusto’s health insurance plans, which cover only 39 states, QuickBooks Payroll’s employee benefits are available in all US states. However, if you’re looking for unique benefits like college savings plans and a health reimbursement option, consider Gusto. Clergy Financial Resources also offers a health reimbursement plan but for an additional fee.
• Expert payroll support: Even with its basic Core plan, you are granted access to payroll support experts you can contact via phone and 24/7 chat if you require troubleshooting assistance and step-by-step help. Although, if you want support from clergy payroll experts, we recommend MinistryWorks (it assigns a dedicated church payroll specialist to its clients) and Clergy Financial Resources (it has clergy tax experts).
• Custom reports: In addition to customizable reporting, QuickBooks Payroll (like Gusto) lets you build and create your own reports directly from its system.

Read Our QuickBooks Payroll Review

Patriot Payroll: Best for Churches Wanting Budget-friendly Flexible Payroll Plans With a DIY Tax Filing Option

Patriot Payroll

Overall Score: 3.49 OUT OF 5

RATING CRITERIA	Church-specific Features	2.00	OUT OF	5
	Ease of Use	3.25	OUT OF	5
	HR Features	1.38	OUT OF	5
	Payroll Features	3.25	OUT OF	5
	Pricing	5.00	OUT OF	5
	Popularity	5.00	OUT OF	5
	Reporting	5.00	OUT OF	5

What We Like

• Reasonably priced
• Unlimited pay runs
• Has flexible plans that include low-cost DIY tax filing and full-service payroll options

What's Missing

• Direct deposit takes four days
• Limited reporting and integration options
• Lacks employee benefits and a dedicated payroll specialist

Patriot Payroll Pricing

• Basic Payroll with DIY tax filings: $10 per month + $4 per employee monthly
• Full Service Payroll: $30 per month + $4 per employee monthly
• Full Service Payroll + HR Software: $36 per month + $6 per employee monthly
• Full Service Payroll + HR + Time and Attendance: $42 per month + $8 per employee monthly

Add-on services

• Multistate tax filings: $12 monthly for each additional state
• 1099 e-filings (for Basic Payroll subscribers only): $20 for up to five 1099 e-filings; an additional $2 per 1099 is required for six to 35 filings (no additional charge for 36 or more)

Patriot Payroll is a good option for small churches as it offers flexible and affordably priced payroll plans. Its basic service that includes DIY tax filings costs only $10 plus $4 per employee monthly. It lets you process unlimited pay runs and pay church employees through direct deposit or manual checks. With its full-service option, you don’t have to worry about tax payments and filings (federal, state, and local) since Patriot Payroll will handle it for you.

Overall, it earned a score of 3.49 out of 5. What prevented this provider from getting higher ratings in our evaluation includes its limited reporting and integration options. While you can set up and create deductions for health insurance or retirement plans, it doesn’t offer employee benefits options like most of the other providers do (particularly Gusto and QuickBooks Payroll, which both have a robust selection). And unlike MinistryWorks, you won’t get a personal payroll specialist to help check your pay runs.

Patriot Payroll Features

• Affordability: Its Basic Payroll option may not include tax filing services, but at $10 plus $4 per employee monthly, the cost is budget-friendly, especially for small ministries. Even if you decide to upgrade to its Full Service Payroll tier, the monthly cost of $30 plus $4 per employee is still quite reasonable. Although if you have the budget to get Patriot’s full payroll services, you may want to consider Square Payroll. It is slightly more expensive if you have 1+ employee (at $35 plus $5 per employee monthly) but you get employee benefits options like healthcare and retirement plans—features that Patriot Payroll doesn’t offer.
• Efficient pay processing: In addition to unlimited pay runs, you can pay church employees via paychecks and direct deposits. However, Patriot Payroll doesn’t have same-day direct deposits like QuickBooks Payroll, plus you have to set up tax codes so that its system can handle minister pay. This is unlike MinistryWorks and Clergy Financial Resources, which have church-specific codes already built into their systems.
• Tax filing services: Patriot Payroll can handle tax payments and filings, including year-end reporting of federal, state, and local taxes—provided you subscribe to its Full Service Payroll plan.
• Expert payroll support: You get expert support that you can contact via phone, email, and chat in case you have payroll-related queries. Best of all, this service is free. However, if you’re looking for dedicated payroll and clergy tax support, MinistryWorks has personal payroll experts who can help review pay runs and Clergy Financial Resources has advisers who can guide you through church-specific tax regulations.

Read Our Patriot Payroll Review

MinistryWorks: Best for Ministries Needing a Dedicated Payroll Specialist

MinistryWorks

Overall Score: 3.44 OUT OF 5

RATING CRITERIA	Church-specific Features	5.00	OUT OF	5
	Ease of Use	4.00	OUT OF	5
	HR Features	2.38	OUT OF	5
	Payroll Features	4.25	OUT OF	5
	Pricing	3.50	OUT OF	5
	Popularity	0.00	OUT OF	5
	Reporting	2.00	OUT OF	5

What We Like

• Automated payroll and tax filings
• Files state new hire reports
• Access to a dedicated payroll specialist

What's Missing

• Charges per pay run
• Limited benefits options
• Very few third-party software integrations

MinistryWorks Pricing*

• Weekly payroll: $8.75 per pay run
• Biweekly payroll: $11.25 per pay run
• Twice monthly payroll: $11.67 per pay run
• Monthly payroll: $17.08 per pay run

*Pricing is from MinistryWorks’ online calculator that shows estimated fees for one employee and for different payroll frequencies. Contact the provider to request a quote.

MinistryWorks is a church payroll software that specializes 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.

Overall, it earned a score of 3.44 out of 5 in our evaluation. MinistryWorks didn’t score as highly as Gusto and QuickBooks Payroll because it doesn’t offer unlimited pay runs, quick direct deposits, or a report builder for creating custom reports. It also has limited integration options with third-party software and the number of up-to-date user reviews available online are slim. However, users appreciate that its software is easy to use and its dedicated payroll specialists are responsive and helpful.

MinistryWorks Features

• Efficient pay processing: With MinistryWorks, you are granted access to church payroll services designed to handle the pay processing and tax calculation needs of ministries. It offers automatic payroll runs, and you can pay employees via manual checks and direct deposits. It does not, however, provide same-day direct deposits as QuickBooks Payroll does. If you want to run payroll as many times as you need without having to pay extra, we recommend any of the other providers included in our guide, all of which offer unlimited pay runs.
• Tax filing services: MinistryWorks handles federal, state, and local payroll tax filings, including year-end tax reporting. You also get tax law compliance counseling and workers’ compensation audit assistance.
• Employee benefits: In addition to pay-as-you-go workers’ compensation and clergy housing allowances, MinistryWorks offers health care reporting and employee eligibility status tracking. However, if you’re looking for more benefits options, consider QuickBooks Payroll or Square Payroll. Gusto is also a good alternative, but its health insurance plans aren’t available in all US states.
• Dedicated payroll support: QuickBooks may include expert payroll support even in its basic Core plan, but MinistryWorks provides a personal payroll specialist who can help review and check pay runs to all of its clients. Note that Patriot Payroll and Square Payroll don’t offer this service, while Clergy Financial Resources and Gusto either charge extra for it or the service is included in the highest tier.

Read Our MinistryWorks Review

Square Payroll: Best for Ministries Wanting to Pay Employee Direct Deposits Via Cash App, Instantly

Square Payroll

Overall Score: 3.43 OUT OF 5

RATING CRITERIA	Church-specific Features	0.00	OUT OF	5
	Ease of Use	4.13	OUT OF	5
	HR Features	3.75	OUT OF	5
	Payroll Features	4.13	OUT OF	5
	Pricing	4.50	OUT OF	5
	Popularity	2.50	OUT OF	5
	Reporting	5.00	OUT OF	5

What We Like

• Affordability
• Automated tax payments and filings
• Unlimited pay runs

What's Missing

• No dedicated church payroll specialist
• Limited report customization
• Phone support requires a customer code; its support team is difficult to reach at times

Square Payroll Pricing

• Pay employees and contractors: $35 per month + $5 per employee monthly
• Pay contractors only: $5 per contractor monthly

With Square Payroll, you are assured that you will have access to affordably priced tools (cheapest on our list for the value it provides—i.e., benefit options that Patriot doesn’t offer) that will help you automatically process payroll, calculate and file quarterly and annual taxes, and manage employee benefits (like health and workers’ compensation). It also allows you to pay employees by paychecks and direct deposits or instantly via Cash App, with no additional charge—faster than other providers on our list (except QuickBooks, which charges a premium for same-day deposit).

Earning an overall score of 3.43 out of 5, Square Payroll didn’t get higher marks in our evaluation because it doesn’t offer church-specific features such as built-in payroll codes for ministers and a dedicated clergy payroll expert (functionalities that MinistryWorks provides). You also can’t create custom reports directly from its system like you can with Gusto and QuickBooks Payroll. Plus, getting phone support can be difficult, with wait times that can be a bit long and a required customer code to contact its support team.

However, we still included Square Payroll in our list of best church payroll services given its low-cost payroll, tax filing, and employee benefits solutions. Many users said that its affordability is one of Square Payroll’s best features. They also like that it has a user-friendly platform that helps them save time when processing payroll.

Square Payroll Features

• Low-cost payroll: Square Payroll offers full-service payroll that is more affordable than other popular providers like Gusto and QuickBooks Payroll. While its monthly fee beyond one employee is slightly more expensive than Patriot Payroll’s Full Service plan ($30 plus $4 per employee monthly), Square provides more features—like multiple payment options and access to healthcare and retirement plans. However, if you’re willing to handle payroll tax filing yourself, then Patriot’s basic tier is a cheaper option, costing only $10 plus $4 per employee monthly.
• Efficient pay processing: With Square Payroll, you get automatic and unlimited pay runs in addition to automated tax payments and filings (including year-end reporting). But if you want a payroll solution with built-in, church-specific codes, then MinistryWorks and Clergy Financial Resources are great alternatives. And while Gusto, QuickBooks Payroll, and Patriot Payroll may not have built-in codes, their online tools are robust enough to handle church payroll services.
• Employee payments through the Square Cash App: Aside from direct deposits and paychecks, you can send employee payments instantly through Square’s Cash App for iOS and Android devices. None of the other church payroll services we reviewed offer this functionality.

Read Our Square Payroll Review

Clergy Financial Resources: Best for Churches Needing HR & Payroll Compliance Help

Clergy Financial Resources

Overall Score: 3.11 OUT OF 5

RATING CRITERIA	Church-specific Features	3.50	OUT OF	5
	Ease of Use	3.75	OUT OF	5
	HR Features	2.38	OUT OF	5
	Payroll Features	3.75	OUT OF	5
	Pricing	3.75	OUT OF	5
	Popularity	0.00	OUT OF	5
	Reporting	2.00	OUT OF	5

What We Like

• Unlimited pay runs
• Offers HR consultation
• Has a 12-month pricing guarantee for new clients

What's Missing

• Expensive for small churches
• Support and health benefits cost extra
• Requires a set-up fee
• Limited benefits, reporting, and third-party integration options

Clergy Financial Resources Pricing

• Starts at $61 per month for up to two employees on a monthly payroll

Add-on services

• Church benefits plans: Ranges from $295–$395 per plan
• Pro Advisor support: $75 for a 30-minute session
• Clergy support on-demand: $355 per year
• Premium church support: 1,200 per year
• HR support plans: Ranges from $120–$720 per year
• Clergy tax preparation: Custom-priced

Clergy Financial Resources is a great option for ministries as an all-inclusive church payroll software that provides HR and clergy tax guidance. It runs unlimited payrolls, files quarterly and year-end tax reports, and calculates and pays both federal and state taxes electronically. You are also granted access to a clergy tax expert and a payroll specialist, plus it offers HR support to help you stay compliant and manage the complexities of church HR—although many of these services cost extra.

Overall, it scored 3.11 out of 5 in our evaluation. This provider ranked the lowest in our list of best church payroll services because its third-party integration, benefits, and reporting options are limited. Clergy Financial Resources also is more expensive than the five other payroll providers in this guide because you have to pay extra for expert support and employee benefits in addition to its church payroll services. And while its online user reviews aren’t as numerous as popular payroll software, most of the feedback is positive with reviewers commending its robust church payroll and tax filing services, including its responsive dedicated specialists.

Clergy Financial Resources Features

• Efficient pay processing: With Clergy Financial Resources, you can run payroll as many times as you need and want. It supports church-specific codes and can handle clergy-related allowances with ease. It also lets you pay employees via direct deposit but doesn’t have QuickBooks Payroll’s same-day options.
• Payroll tax payments and filings: In addition to electronic payroll tax payments (federal, state, and local), Clergy Financial Resources can handle quarterly and end-of-year tax reporting. However, if you’re looking for a more cost-efficient option, consider Square Payroll as it provides full-service pay processing and tax filing services for only $35 plus $5 per employee monthly.
• Clergy tax, payroll, and HR compliance support: You get a wide range of support services from Clergy Financial Resources to help you stay compliant as you tackle the intricacies of handling church-related tax, payroll, and HR issues—it only services churches. While you have to pay extra for these, Clergy Financial Resources’ church compliance support is more extensive than that from providers like Gusto, Square Payroll, and Patriot Payroll.

Read Our Clergy Financial Resources Review

How We Evaluated the Top Church Payroll Services

We compared 13 payroll providers that offer church payroll software, looking for functionalities we believe are most important for churches and 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 flexible pricing options affordable for small businesses.

Click through the tabs in the box below to view our full evaluation criteria.

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 software 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 free trial today.

Visit Gusto