Just like any other organizations, churches and ministries also need to process their payroll and comply with IRS tax rules. However, church payroll requirements are somewhat different from that of small businesses. Aside from the usual payroll processing and tax withholding and filing, there are other features that make running church payroll easier, like church-specific tax law expertise.
Some church payroll services have experts on staff that handle payroll processing completely, while others guide its users. We evaluated a dozen providers, including free or cheap do-it-yourself options, and picked the best church payroll services you should consider.
Top Payroll Services for Churches and Ministries
Church Payroll Provider | Best for |
|---|---|
(Best Overall) Churches and ministries looking for basic payroll, tax, and HR solutions, including church-specific features for an affordable price | |
Churches that process payroll to pay their employees the same or next day | |
Small churches and ministries that need to run basic payroll for hourly workers | |
Low-cost payroll software for churches that need either payroll or tax assistance or both | |
Ministries without staff to run payroll who need a dedicated payroll processor | |
Churches that need a one-stop shop payroll provider that offers compliance guidance |
How We Chose the Top Church Payroll Services
We compared the best payroll services that offer church payroll software, according to features we believe are most important for churches and ministries. We included flexible pricing options that are affordable to higher-end providers for those that want a full service. In addition, we looked for payroll and tax features specific to church payroll plus attributes that made the service easy to use.
We were able to narrow our list of a dozen providers down to six, and Gusto scored the highest. It provides church-specific services aside from the basic payroll, tax, and HR tools for an affordable price. It also runs unlimited payroll, files taxes, pays church employees, and prepares W2 and 1099 forms with no additional cost.
RUBRIC SCORECARD CRITERIA:
20% of Overall Score
We gave priority to those that offer automatic payroll runs, direct deposit with an option to process paper checks, and access to tax payment and filing, including year-end forms filing (W-2s and 1099s).
20% of Overall Score
Payroll service and software should be easy to access, simple to set up, and have a user-friendly interface. A dedicated representative, as well as employer ID and tax set-up assistance, are top criteria. Sometimes, churches are on the lookout for HR advising and online resources or how-to guides that are available.
20% of Overall Score
We looked at the monthly implementation costs, processing costs, set-up, and year-end fees. Preference was given to providers that are affordable since churches and ministries are not-for-profit organizations.
15% of Overall Score
We gave priority to church payroll services that have expertise in the unique tax treatment of clergy housing allowances and exemptions. Some software have features that allow you to account for these special clergy tax situations. Aside from that we also looked into providers that integrate well with existing church accounting systems and/or time clocks.
10% of Overall Score
Online onboarding, which means giving employees the option to fill out forms like W-4 and W-9 electronically, is the top criterion; following closely behind is the ability to offer a self-service portal that employees can use to see payments made, edit information, and/or print forms.
10% of Overall Score
We considered user reviews, including that of our competitors based on a 5-star scale; any option with an average of 4+ stars is ideal. Also, any software with 1,000+ reviews on any third-party site is preferred. We also searched for reviews left specifically by churches.
5% of Overall Score
Software with 60+ canned reports (preformatted reports) is considered robust, but also, those that are customizable and/or have functionality allowing users to build their own reports.
Gusto
PROS
- Unlimited and automated payroll runs
- Employee self-onboarding portals
- Third-party integrations: Aplos, QuickBooks, Xero, Clover, TSheets
CONS
- No dedicated payroll specialist
- Workers' benefits and compensation processing is limited to 24 states
- Time tracking is not included in the Core plan
| RATING CRITERIA | Pricing | 5 | OUT OF | 5 |
| Church-specific Features | 2.67 | OUT OF | 5 | |
| HR Features | 4 | OUT OF | 5 | |
| Popularity | 5 | OUT OF | 5 | |
| Reporting | 4 | OUT OF | 5 | |
| Payroll Features | 4.75 | OUT OF | 5 | |
| Ease of Use | 3.63 | OUT OF | 5 |
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.
Gusto Pricing
- Core Plan: $39 per month plus $6 per employee
Gusto would cost $99 per month for 10 employees, which equates to $1,188 per year–cost-wise, falling in between the lowest and highest cost providers on our list.
Gusto Features
- Unlimited payrolls
- All 50 states, plus federal and local tax payment and filing
- Free support in church payroll setup
- Year-end tax reports (W-2s and 1099s)
- Direct deposit and manual check capabilities
- Online employee set up and accounts
- Track Sick and Vacation time
- Integrations with QuickBooks, Aplos, and other time-tracking software
QuickBooks Payroll
PROS
- Unlimited payroll runs
- Automates tax calculations, payment, and filing for federal and state taxes
- Manages garnishments, deductions, and health benefits
CONS
- No new hire reporting
- Limited third-party integrations
- No online onboarding
| RATING CRITERIA | Pricing | 4 | OUT OF | 5 |
| Church-specific Features | 6.67 | OUT OF | 5 | |
| HR Features | 3.75 | OUT OF | 5 | |
| Popularity | 3.75 | OUT OF | 5 | |
| Reporting | 4 | OUT OF | 5 | |
| Payroll Features | 4.25 | OUT OF | 5 | |
| Ease of Use | 4.25 | OUT OF | 5 |
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.
QuickBooks Payroll Pricing
- Core Plan: $45 monthly + $4 monthly per employee
QuickBooks Payroll offers three plans to choose from: Core, Premium, and Elite. The Core plan covers all the payroll basics and charges $85 per month for 10 employees– $1,020 annually.
QuickBooks Payroll Features
- Runs payroll (has autopay) and files all taxes
- Direct deposit
- Online employee portal
- Prepares year-end tax reports for free
- Offers health benefits, 401(k), and workers’ compensation
- No contract or startup fees
- Integrates with QuickBooks accounting software
- Customizable and downloadable payroll reports
- Expert product support
Square Payroll
PROS
- Timecard integration
- Square Team mobile application access
- Automatic quarterly and annual tax filings
CONS
- No dedicated account specialist
- No new hire reporting
| RATING CRITERIA | Pricing | 4.5 | OUT OF | 5 |
| Church-specific Features | 0 | OUT OF | 5 | |
| HR Features | 3.75 | OUT OF | 5 | |
| Popularity | 2.5 | OUT OF | 5 | |
| Reporting | 3 | OUT OF | 5 | |
| Payroll Features | 4.5 | OUT OF | 5 | |
| Ease of Use | 3.13 | OUT OF | 5 |
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.
Square Payroll Pricing
- Square Payroll Plan: $29 monthly + $5 monthly per employee or contractor
A church with 10 employees or contractors would pay $79 per month or $948 per year, less than Gusto but more than Patriot’s full-service option.
Square Payroll Features
- Automatically runs payroll
- Automatically calculates, files, and pays federal and state taxes
- Pays employees using direct deposit, check or cash app
- Automatically syncs workers’ compensation and health benefits with payroll
- No commitment, cancel anytime policy
Patriot Payroll
PROS
- Low cost
- Offers online and mobile payroll processing
- Integrates with QuickBooks + seamlessly with its own accounting software
- No setup costs
CONS
- Only does tax calculations
- Only Full Service, which costs extra, has year-end report prep
- Limited reporting
| RATING CRITERIA | Pricing | 5 | OUT OF | 5 |
| Church-specific Features | 2.67 | OUT OF | 5 | |
| HR Features | 2 | OUT OF | 5 | |
| Popularity | 5 | OUT OF | 5 | |
| Reporting | 3 | OUT OF | 5 | |
| Payroll Features | 3.25 | OUT OF | 5 | |
| Ease of Use | 3.25 | OUT OF | 5 |
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.
Patriot Payroll Pricing
- Basic Plan: $10 monthly + $4 per employee (Payroll only)
- Full Service: $30 monthly + $4 per employee (Payroll and tax compliance)
The Full-Service plan at $70 per month for 10 employees would be $840 per year–the most affordable service on our list.
Patriot Payroll Features
- Runs payroll and performs all calculations
- Option to sign up for Full-Service payroll or file your own taxes to save money
- Unlimited pay runs
- 2-day direct deposit
- Live phone support
- Integrates with many popular software such as QuickBooks
MinistryWorks
PROS
- Provider does payroll for you
- Calculates, pays, and files taxes (no extra cost)
- Files state new hire reporting forms
CONS
- In-house printing of paper checks is not free
- Not much third-party software seamless integration
- Charges per payroll run
| RATING CRITERIA | Pricing | 2.75 | OUT OF | 5 |
| Church-specific Features | 4.67 | OUT OF | 5 | |
| HR Features | 5 | OUT OF | 5 | |
| Popularity | 0 | OUT OF | 5 | |
| Reporting | 0 | OUT OF | 5 | |
| Payroll Features | 3.25 | OUT OF | 5 | |
| Ease of Use | 4.75 | OUT OF | 5 |
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.
MinistryWorks Pricing
MinistryWork costs $26 per weekly payroll for 10 employees or $1,346 annually; this includes W2 tax preparation work. You’ll need to request a quote to get a final cost for your business.
MinistryWorks Features
- Has a self-service portal
- Automated payroll
- Direct deposit and manual check capabilities
- Files year end tax forms (W-2s and 1099s)
- Offers tax law compliance counseling
- Workers’ compensation audit assistance
- Online training and support
- Personal payroll specialist
Clergy Financial Resources
PROS
- Offers HR consultation
- Unlimited payroll runs
- Has a dedicated clergy tax expert and payroll specialist
CONS
- It has a setup fee
- Pricey for just one to two employees
- Does not file new hire reporting forms
| RATING CRITERIA | Pricing | 2.75 | OUT OF | 5 |
| Church-Specific Features | 4.67 | OUT OF | 5 | |
| HR Features | 2.38 | OUT OF | 5 | |
| Popularity | 0 | OUT OF | 5 | |
| Reporting | 0 | OUT OF | 5 | |
| Payroll Features | 3.75 | OUT OF | 5 | |
| Ease of Use | 3.88 | OUT OF | 5 |
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.
Clergy Financial Resources Pricing
Clergy Financial Resources’ basic plan is relatively more pricey than its competitors on the list at $224 monthly ($2,688) for 10 employees paid weekly and $125 monthly ($1,500 annually) for 10 employees paid biweekly–the more pay runs, the more it costs. You also need to pay a setup fee of $150. It also offers a 12-month pricing guarantee with no additional costs for year-end reporting.
Clergy Financial Resources Features
- Runs unlimited payroll and files taxes
- Pays employees through direct deposit
- Prepares quarterly and year-end tax filings
- Prepares and mails year-end forms at extra cost
- Live support by phone, chat and email
- Guaranteed accurate tax calculations
For a wider range of payroll options, check out our buyer’s guides on the best payroll services and best payroll software.
To learn about specific payroll requirements for churches, check out our industry-specific payroll guide.
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, but more than affordability, they should have church-specific features that help churches pay clergy and non-clergy employees efficiently, 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 since the service does everything for you, and the price is reasonable when compared to other church payroll services. Sign up to try it today.
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