Payroll Solutions for Churches and Charities

Running payroll for a church or charity comes with unique challenges – from handling clergy housing allowances to ensuring tax-exempt staff are managed correctly. Thankfully, there are payroll platforms tailored to the needs of nonprofits and religious organizations. Below we highlight several such platforms (and their pros and cons), so you can keep your focus on your mission instead of payroll headaches.

Gusto – Full-Service Payroll with Nonprofit Features

Gusto is a popular full-service payroll platform known for its ease of use and comprehensive features. While not built exclusively for churches, it supports clergy-specific needs like pastor housing allowances and tax exemptions. Gusto automates payroll taxes (filing federal, state, and local forms) and offers unlimited payroll runs, making it a convenient choice for small charities and churches. It also integrates with nonprofit accounting tools (e.g. Aplos and QuickBooks), which helps link payroll data to fund accounting and donor reports.

Gusto Pros:

• Supports clergy housing allowances and tax-exempt minister compensation out of the box.
• Unlimited pay runs and automatic tax filing included – saving time and ensuring compliance.
• User-friendly self-service for employees and admins; integrates with nonprofit accounting software like Aplos for seamless bookkeeping.
• Offers additional HR tools (benefits, onboarding, PTO tracking) useful as your organization grows.

Gusto Cons:

• No dedicated church payroll specialist – support is general, so you won’t get clergy-specific advice by default.
• Some advanced features (time tracking, advanced HR) are only in higher-priced plans.
• Health insurance benefits are not available in all states (a consideration if your ministry offers health plans)

OnPay – Nonprofit-Focused Payroll with Clergy Tax Handling

OnPay is a cloud-based payroll service that explicitly caters to ministries and nonprofits. It handles both clergy and non-clergy payroll seamlessly – for any worker you mark as clergy, OnPay automatically exempts them from FICA (Social Security/Medicare) and FUTA taxes as appropriate. This ensures pastors and ministers are taxed correctly without extra hassle. OnPay’s single plan includes full-service payroll with unlimited runs and multiple pay options (direct deposit, checks, even prepaid debit cards). It also provides basic HR tools and benefit management in all 50 states, plus six levels of user permissions so you can delegate payroll tasks securely.

OnPay Pros:

• Built-in clergy tax support: automatically handles ministerial tax exemptions (no FICA/FUTA) for clergy members.
• Unlimited payroll runs and flexible payment methods (direct deposit, checks, debit cards) at no extra cost.
• Compliance safeguards: proactive alerts for missing forms or onboarding steps help you stay in line with regulations.
• Easy delegation: robust permission controls let you involve different staff/volunteers in payroll or HR as needed without losing oversight.

OnPay Cons:

• Limited integrations: OnPay does not currently integrate with specialized church management systems, which can be a drawback if you want it to sync with your other church software.
• No 24/7 support: Live phone support is weekdays only – you won’t have weekend phone help if a payroll emergency arises.
• Lacks tiers; one plan keeps it simple, but it means no lower-cost option if you need only very basic features (though pricing is flat and reasonable).
• Some advanced HR add-ons (like consulting with HR experts) cost extra, which may not be ideal for tight church budgets.

MinistryWorks – Church-Exclusive Payroll Service with Expert Support

MinistryWorks is a payroll platform designed specifically for churches and religious organizations. Backed by Brotherhood Mutual, it understands clergy pay inside and out – from housing allowances to the dual tax status of ministers. MinistryWorks handles all payroll processing and takes care of federal, state, and local tax filings for you (including specialized filings like clergy SECA taxes and ACA reports). A standout feature is their personalized support: every client gets access to dedicated payroll specialists who are well-versed in church payroll rules and can guide you through complex situations. This “white glove” approach brings peace of mind to church administrators.

MinistryWorks Pros:

• Purpose-built for churches: explicitly addresses clergy housing allowances, ministerial tax exemptions, and other ministry-specific payroll needs.
• Expert guidance: offers a personal payroll specialist who understands church regulations – they even help double-check pay runs and counsel on compliance.
• Full compliance service: automatically files all payroll taxes (federal, state, local) and handles year-end W-2s/1099s, reducing error risk for your church.
• Ease of use: Simplified payroll workflows and knowledgeable support make it user-friendly, even if you’re not a payroll expert.

MinistryWorks Cons:

• Pay-per-run pricing: Unlike many competitors, MinistryWorks limits the number of pay runs and charges per payroll run (no unlimited runs). Churches running very frequent payrolls (or lots of special pay batches) might incur higher fees.
• No instant direct deposit: Direct deposits aren’t same-day; you may have to plan payroll a bit in advance (minor inconvenience noted by some users).
• Fewer software integrations: MinistryWorks is a more self-contained service – it doesn’t connect with as many third-party accounting or church management systems as some other platforms.
• Basic feature set beyond payroll – it focuses on core payroll and compliance, with relatively limited HR add-ons compared to broader solutions.

SurePayroll (Paychex) – Budget-Friendly Payroll for Small Churches

SurePayroll is an online payroll service (part of Paychex) that offers a special focus on churches and religious institutions. It simplifies paying both clergy and lay staff, automatically calculating and filing taxes so you don’t need in-house expertise. SurePayroll supports clergy-specific compensation, allowing you to set up pastors’ housing allowances easily. With this platform you can choose full-service payroll or a lower-cost DIY tax filing plan, making it flexible for tight church budgets. Unlimited pay runs are included even in the basic plan, and the interface is designed to be simple for non-accountants.

SurePayroll Pros:

• Affordable plans: very cost-effective for small churches, with options to save by handling tax filings yourself or let SurePayroll do it for you.
• Clergy allowance support: built-in option to handle clergy housing allowances and properly segregate that income for tax purposes.
• Full-service features: automatic calculation and payment of payroll taxes and year-end forms are available, removing compliance burden from church staff.
• Unlimited payroll runs: run payroll as often as needed with no extra charge, which is great for churches that pay contractors or stipends on varied schedules.
• Easy to use: mobile-friendly tools and a simple interface make it approachable – you don’t need to be a financial pro to run payroll.

SurePayroll Cons:

• Extra fees for add-ons: Handling multiple state tax filings or certain integrations can incur additional fees. If your ministry has staff across several states, costs might rise.
• Limited integrations: SurePayroll doesn’t natively connect with most church management or fund accounting systems (integration options are limited without paying for custom setups).
• Fewer church-specific extras: Aside from housing allowance and basic minister tax settings, it’s not as specialized as some church-only services (no dedicated church advisor included).
• The DIY plan requires you to file taxes yourself, which could be daunting if you’re not comfortable with payroll taxes (the full-service plan avoids this issue).

ACS Realm Payroll – Integrated Church Management with Payroll

Realm by ACS Technologies is a comprehensive church management system, and it includes a payroll module built specifically for churches as part of its accounting tools. Realm’s payroll lets you process staff paychecks while accommodating church-specific requirements like ministerial allowances and special tax rules. Because it’s integrated with the larger Realm platform, your payroll data ties directly into fund accounting (general ledger) and the staff records in your church database. This means housing allowances, benefits, and reimbursements can be tracked in one place alongside your other church finances. It’s essentially a one-stop solution for churches that want administration, accounting, and payroll under one roof.

ACS Realm Payroll Pros:

• Built for church needs: Realm’s payroll is part of a church-specific system, so it natively handles clergy tax settings and housing or auto allowances for ministers.
• All-in-one integration: Payroll entries automatically post to Realm’s fund accounting ledgers, and employee data is shared with your church HR records – no double entry between systems.
• Time-saving automation: Calculates withholdings and deductions, prints checks or does direct deposit, and even handles tax e-filing (via integrated services) to streamline the payroll process.
• Comprehensive platform: Along with payroll, you get the benefits of Realm’s broader features (donations, membership, events), which can improve overall administrative efficiency in a mid-sized church.

ACS Realm Payroll Cons:

• Requires Realm subscription: The payroll module isn’t a standalone product – you need to be using Realm’s church management suite. This could be costly for small churches that only want payroll, since Realm’s pricing bundles many features.
• Learning curve: Realm is powerful software with many modules; new users may need training to fully utilize the payroll features within the broader system. It’s not as plug-and-play as some dedicated payroll-only services.
• Less flexible outside the ecosystem: If your church already uses different accounting or management software, adopting Realm payroll would mean switching systems, as it’s most effective when used as part of the ACS ecosystem.
• Primarily focused on U.S. churches (handles U.S. payroll taxes); not suitable for international organizations.

Church Windows Payroll – Church Management Software with Payroll Module

Church Windows is a long-standing church management software that includes a robust Payroll module for handling church staff pay and taxes. It’s available as a locally-installed program or via a cloud-hosted option, and it integrates with Church Windows’ fund accounting and donations modules. With Church Windows, you can generate payroll checks, direct deposit stubs, all required tax forms, and even track pastor allowances within the system. The software keeps federal and state tax tables up-to-date, helping churches remain compliant without manual updates. Church Windows is known for reliable support and has been trusted by many churches for decades for both finance and membership management.

Church Windows Payroll Pros:

• Church-specific functionality: Built expressly for churches – handles clergy allowances, prints W-2s, and supports fund accounting integration so payroll expenses tie into your ministry’s books.
• Updated tax tables: The software provides regular updates to federal and state tax tables and forms, so your payroll calculations and reports stay current with tax law changes.
• Integrated solution: Payroll data flows into the Church Windows Accounting module, and you can link with Donations records, giving you a central hub for church finances.
• Flexible deployment: Can be used on desktop or accessed via the web, giving churches choice based on their tech preferences.
• Strong support and community: Users praise the company’s support team for being responsive and knowledgeable about church scenarios, which eases the learning process for new users.

Church Windows Payroll Cons:

• Initial learning curve: As a comprehensive church management system, it can take some time to learn the interface and setup (especially for those new to accounting software). However, training resources are available to help.
• Modular cost structure: You may need to purchase or subscribe to multiple modules (Membership, Accounting, Payroll, etc.) for full benefit. The costs can add up, and the cloud subscription (if chosen) isn’t cheap – potentially a drawback for very small congregations.
• Manual tax filing (optional e-file): While Church Windows prepares all payroll tax forms, you typically file them yourself (or use a partner service like Aatrix for e-filing). This is less automated than a full-service payroll provider that files on your behalf.
• Windows-centric: The desktop version runs on Windows OS. Mac users would need to use the web version or a compatibility workaround.