14 Best Church Payroll Software Reviewed For 2025
10 Best Church Payroll Software Shortlist
Here's my pick of the 10 best software from the 16 tools reviewed.
Our one-on-one guidance will help you find the perfect fit.
Church payroll is often a mess—especially if you’re using generic tools or still doing parts of it by hand:
You waste hours, risk tax violations, and can still end up unsure if it’s all correct.
Why? Because churches aren’t like other employers. And if your payroll system doesn’t account for those differences, you’re flying blind. With that in mind... here’s a ranked list of payroll software that actually understands how churches work.
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The 10 Best Church Payroll Software Solutions Summary
| Tool | Best For | Trial Info | Price | ||
|---|---|---|---|---|---|
| 1 | Best for global payroll and compliance | Free demo available | Flat rate user pricing, with a free version for businesses with up to 200 people | Website | |
| 2 | Best for unlimited payroll runs | 30-day free trial | From $40/month + $6/user/month | Website | |
| 3 | Create an online database for your payslips and financial records | 30-day free trial | From $2/month (for 3 months, then $20/month) | Website | |
| 4 | Best for US-based churches | 30-day free trial | From $4/employee/month + $17/month base fee | Website | |
| 5 | Run payroll with a solution that files your taxes for you | Free demo available | From $40/month + $6/user/month | Website | |
| 6 | Schedule direct deposits in advance and automate the payroll process | You can schedule a demo and try the solution out for free for three months. | custom pricing upon request | Website | |
| 7 | Run payroll and benefit from dedicated support | You can access a demo and request a free trial. | from $279/month | Website | |
| 8 | Set up automated tax payments and control your finances | Free plan available | From $16/user/month | Website | |
| 9 | All-in-one church software with good payroll features | Download free demo | costs from $395 | Website | |
| 10 | Best for tax penalty protection | 30-day free trial | From $30/user/month | Website |
Reviews Of The 10 Best Church Payroll Software Solutions
Here’s a brief description of each church payroll platform to showcase each tool’s best use case, some noteworthy features, and screenshots to give a snapshot of the user interface.
Deel is a global payroll and compliance platform that can be utilized by various organizations, including churches, to facilitate the hiring, onboarding, and payment of employees and contractors around the world.
The platform offers tools for creating contracts compliant with local laws, processing payroll, and handling tax documentation, which can be particularly useful for churches with international missionaries or remote workers. Deel's ability to handle multiple currencies and payment methods, including cryptocurrencies, may also be beneficial for churches with diverse payment needs.
Deel integrates with multiple solutions, including Xero, BambooHR, Lever, Greenhouse, Workday, Quickbooks, Netsuite, Rippling, ADP, and Paychex.
OnPay is an online payroll service that offers solutions for payroll processing, HR, and benefits management. It aims to simplify these processes with features like automatic tax calculations, payroll setup, data migration, and integration with various business applications such as QuickBooks and Xero.
The platform simplifies the complex tax scenarios often faced by churches. For instance, OnPay automatically handles situations specific to clergy compensation and taxes, non-clergy members, and housing allowances. It also offers unlimited payroll runs.
Integrations include QuickBooks, Xero, Deputy, Guideline, Vestwell, Mineral, Magnify, and more.
Xero
Create an online database for your payslips and financial records
Xero is an online accounting solution that doubles as a nonprofit accounting software. The platform has a beautiful build that’s easy to navigate and understand, so you should be able to find and use most of its features with minimal training.
The payroll tool helps you set up recurring pay runs and keep basic pay records. You can enter employee hours, set up and update hourly rates, and calculate deductions. You can send your staff payslips via email or you can print them. The platform stores the information online, so your church members can check their payslips using mobile devices.
Xero integrates with dozens of solutions, including EzzyBills, Stripe, Deel, HubSpot, Square, PayPal, and Zapier.
Patriot Payroll is an online payroll service that offers an easy-to-use platform tailored for small organizations, including churches. It streamlines payroll management, providing a cost-effective and reliable solution for handling payroll processes efficiently.
Patriot includes features essential for managing church payrolls, such as automatic tax calculations, direct deposit, and an employee portal for accessing pay stubs and W-2 forms. The full-service payroll option takes care of all federal, state, and local tax filings, ensuring compliance and reducing administrative burdens.
Additionally, its customizable pay rates and payroll reports allow for flexible and detailed management of church finances. Integrations include QuickBooks, TSheets, Gusto, Square, FreshBooks, and Xero.
Gusto is a popular HR and payroll management solution. The platform is a great choice for modern churches because it enables you to set your employees up with benefits and manage paid time off. And the solution also creates an online database for your staff’s pay stubs, so they can check them out using mobile devices.
The great thing about using this app is that it files your taxes for you. Every time you run payroll, the solution files your tax sheets with the right federal or state agencies. The software keeps track of tax changes, so you don’t have to worry about misfilings.
Integrates with multiple apps, including Aplos church software, 15Five, 7Shifts, ActiveCampaign, Asana, Clover, QuickBooks, and Bonusly.
CDM+ is an online church management software that enables clergy members to speed up their payroll process. The software creates an online portal for your employee so they can access their pay history, pay stubs, withholdings and deductions.
The solution also allows you to schedule direct deposits in advance, so you can automatically run payroll during bank holidays. The tool also helps you with other financial aspects, such as online giving tracking or fund accounting, and enables you to generate custom reports.
This software has a mobile-friendly version, so you can access it on any device, from anywhere, at any time.
Church Windows is a church management software with a good payroll feature. This solution creates a centralized location for all your accounting and financial information, so you can gain visibility into your finances and simplify your existing processes.
The highlight of using this platform to run payroll is that it allows you to generate checks, tax forms, reports, and allowances with ease. The Federal and State tax tables are updated when necessary, so you don’t need to change them yourself. You can also transfer your payroll information into the accounting module.
Church Windows has a slight learning curve, but the software’s support team can guide you through the payroll process.
Wave is a cloud-based church software that allows you to check your accounting and financial information from wherever you are. The platform covers all the financial needs of a church, from payroll service to online donation processing and bank connections.
This software stands out thanks to its clean layout. Every feature and functionality is highlighted accordingly, so even people who are not tech-savvy can quickly learn their way around this tool.
The payroll feature allows you to generate W2 and 1099 forms in preparation for tax season and deposit money into your staff’s bank accounts. Wave also enables you to set up automated tax payments for specific states in the US.
PowerChurch Plus is an all-in-one church management software with dedicated payroll features. The solution helps you with church bookkeeping, financial management, as well as other aspects of church management.
This software creates a database for all your financial and personal records, making it easy to access information. You can also run payroll and pull reports on your contributions and accounts payable throughout the fiscal year.
The solution’s Knowledge Base helps you set up and maintain payroll according to federal and state laws. You can also access detailed guides and screenshots to speed up the setup process.
PowerChurch software integrates with several apps, including Vanco, Dynamic Systems, Avery, SimpleTexting, Clockify, and Constant Contact.
QuickBooks Payroll is a payroll management tool that assists businesses with automated tax calculations, filings, and time tracking. It stands out for its tax penalty protection feature, which safeguards businesses against potential tax penalties, positioning it as a reliable solution for tax compliance and protection.
I chose QuickBooks Payroll for church payroll software because of its comprehensive service offerings and user-friendly interface, which are particularly suited to the unique needs of church payroll management. What makes QuickBooks Payroll different is its automatic tax calculations and filings, which significantly reduce the risk of errors and penalties, a critical factor for non-profit entities like churches. I believe QuickBooks Payroll is best for tax penalty protection due to its robust compliance features and seamless integration with other QuickBooks products, catering to various business stages and industries.
QuickBooks Payroll integrates with 650 popular business apps including PayPal, Veem, Google Sheets, SaasAnt, Expensify, PaperEntry, BillBjorn, TimeSaver, ClockShark Time Tracking, Gusto, Run Powered by ADP, Guideline 401(k), Fundbox, Bill.com, and many others.
Other Church Payroll Options
Here are a few more church payroll tools that didn’t make the top list.
- QuickBooks Online
Automate your tax filing and payroll processes
- Rise
Put payroll on autopilot and receive notifications if you make errors
- BambooHR
Online HR platform with a powerful payroll feature that helps you manage your team’s pay.
- Hubstaff
Employee monitoring platform that enables you to track your staff’s activity, create invoices, and automate your payroll process.
- Fellowship One
Set up payroll and clergy allocations with a step-by-step guide
- Wagepoint
Payroll simplification solution that helps community leaders run payroll and get support when filing their taxes.
Selection Criteria for Church Payroll Software
Here’s how I evaluate church payroll software—no buzzwords, no fluff. This category of software should solve real, everyday problems for church leaders and admins. That means automating repetitive work, staying compliant, keeping records clean, and helping your team spend less time on operations and more time on ministry.
Yes, my team and I have personally tested and researched every product here.
Core Church Payroll Software Functionality – 25% of total score
Common features for church payroll software typically include direct deposit, tax filing, W-2/1099 generation, housing allowance tracking, time tracking, benefits administration, staff classification (clergy vs. non-clergy), payroll scheduling, reporting tools, and self-service portals.
To be considered for inclusion on my list of the best church payroll software, the solution had to support the ability to fulfill common use cases.
- Paying clergy and non-clergy employees correctly and on time
- Managing withholdings and deductions for housing allowances
- Filing federal and state taxes accurately
- Generating year-end tax forms for staff and contractors
- Tracking hours, PTO, and other time-related data
Additional Standout Features – 25% of total score
- Built-in support for clergy-specific exemptions and allowances
- Automated reminders for quarterly tax payments
- Integrations with church accounting tools like Aplos or QuickBooks
- Role-based access controls for treasurers, pastors, and admins
- Real-time dashboards with audit trails for every payroll action
Tools like Gusto and MinistryWorks offer features like automatic housing allowance breakdowns or built-in pastoral pay structures—things generic payroll software never touches. I test for how well these features actually work in real-world church contexts.
Usability – 10% of total score
- Clear distinction between clergy and lay employee workflows
- No buried menus—common tasks like running payroll should be front and center
- Simple toggles to turn features like housing allowance on/off
- Intuitive interfaces for staff to access pay stubs or update info without help
- Clean dashboards that highlight errors, compliance issues, or tasks due
Onboarding – 10% of total score
- Pre-built templates tailored for churches (not just generic orgs)
- Step-by-step guided setup wizards for church-specific settings
- Access to recorded webinars or short, practical training videos
- Live chat or chatbot to answer questions during setup
- Migration tools for importing staff data and payroll history from other platforms
Customer Support – 10% of total score
- Access to real humans who understand church-specific needs
- Fast response time via chat, email, or phone
- Support hours that align with typical church office hours
- Documentation and FAQs that explain clergy pay rules in plain English
- Ongoing help—not just during onboarding, but when things break mid-year
Value For Money – 10% of total score
- Transparent pricing with no surprise fees for tax filings
- Tiered plans that scale with staff size
- No unnecessary add-ons or forced bundling with unrelated features
- A clear ROI—saves staff time or reduces risk of costly compliance errors
- Discounts or custom pricing for churches or nonprofits
Customer Reviews – 10% of total score
- Strong track record with churches specifically—not just generic orgs
- Consistent praise for ease of setup and ongoing use
- Positive feedback about how well support handles clergy-specific questions
- Fewer complaints about surprise costs or buggy updates
- Loyalty—users sticking with the platform for multiple years
This is the bar. Anything that doesn’t meet it gets cut.
How to Choose Church Payroll Software
As you work through your own unique software selection process, keep the following points in mind:
- Clergy-Specific Payroll Support:
Churches don’t follow the same payroll rules as for-profits. Clergy pay, housing allowances, dual tax status—if your payroll software can’t handle those out of the box, you’re setting yourself up for errors, IRS issues, or both. Make sure the platform supports church-specific configurations without you needing to hack together workarounds. - Tax Compliance and Filing:
Churches face different filing responsibilities than standard businesses, especially with exempt vs. non-exempt staff, parsonage allowances, and self-employment tax. Look for tools that clearly walk you through state and federal tax setup and offer automated filing. If you’re still mailing forms or manually uploading to government portals, you’re wasting time and increasing your risk. - Ease of Use for Non-Financial Staff:
Most churches don’t have a full-time payroll manager. Often it’s an office admin, an executive pastor, or a volunteer. Your payroll system needs to be usable without a finance degree—clean layout, smart defaults, clear next steps. If a part-time staffer can’t run payroll without calling support, that’s not a good sign. - Seamless Integration with Church Accounting Tools:
Juggling two disconnected systems for payroll and accounting leads to mistakes and double entry. Look for church payroll software that integrates natively with platforms like Aplos, PowerChurch, or QuickBooks for Churches. Bonus if it automatically syncs GL codes and categorizes clergy allowances properly. - Scalability for Multi-Staff Churches:
A lot of platforms work fine for one or two employees, but break down once you have ten staff, multiple campuses, or part-time roles with weird schedules. Check if the system supports role-based access, department-specific reporting, and flexible payroll schedules—so you’re not stuck switching again when your team grows.
Trends in Church Payroll Software for 2025
Church payroll software is finally catching up. For years, we tried to jam church staff into corporate HR tools that weren’t built for ministry. That era’s ending. In 2025, the best systems are purpose-built—designed for how churches actually run, legally and financially.
Here’s what’s changing—and what’s already outdated.
1. Compliance Can’t Be an Afterthought
- State-Specific Logic Is Now Built-In. The good tools no longer act like every church is the same. Housing allowances, dual-status clergy, multi-state rules—it’s all automated now. If you still need to Google IRS rules before payday, your software’s outdated.
- W-2s and 1099s Shouldn’t Need Fixing. End-of-year filing should just work. No more hand-editing forms to reflect clergy exemptions. If your platform can’t handle that by default, it’s behind.
2. Payroll and Finance Are Merging
- Integrated Accounting Is the New Normal. Churches are ditching multiple systems. Payroll, fund accounting, donor tracking—it’s all rolling into one platform. One system. One audit trail. That’s where we’re headed.
- Flexibility Is Winning Over Simplicity. Churches don’t fit into neat little boxes. You’ve got volunteers, part-time staff, multiple roles. Your payroll tool needs to handle that. If it can’t support different job codes, pay groups, or ministry teams, you’ll outgrow it fast.
3. User Experience Finally Matters
- Mobile Access Isn’t Optional. You’re not always in the office. Payroll has to work from a phone, in a meeting, or on a Sunday afternoon. Mobile-first isn’t a bonus—it’s a must.
- The UI Shouldn’t Slow You Down. You shouldn’t need a manual. Clear dashboards, fast load times, five clicks to finished payroll. That’s the new bar. If your volunteer treasurer can’t figure it out? It’s the wrong tool.
4. Integration Is Now Table Stakes
- Church Management + Payroll = Required. Your ChMS should talk to your payroll system. Staff roles, access, giving records—it all needs to sync. No more double entry. No more import/export games.
- Reports Should Serve the Finance Committee, Not Just the IRS. You need ministry-aware reports—by department, by role, clergy-specific. Real-time, exportable, readable. Spreadsheets aren’t cutting it anymore.
5. What’s On the Way Out
- Generic Templates. If your software treats your church like a gym or law firm, it’s not built for you.
- Manual Overrides. Flexibility shouldn’t mean fixing broken logic every pay cycle. If you’re babysitting the numbers, the system’s failing.
Bottom line: The best church payroll software in 2025 doesn’t do more. It does the right things—things built for ministry. The rest is noise.
What is Church Payroll Software?
Church payroll software is a tool that helps churches pay their staff correctly and on time—especially when dealing with tricky stuff like housing allowances, part-time pastors, or paying both employees and guest speakers. It handles paychecks, tax forms, and withholdings so you don’t have to do it all in spreadsheets or guess at IRS rules.
Think of it like having a church-savvy bookkeeper built into your computer.
Features of Church Payroll Software
When you're leading a church, the last thing you want is to be buried in admin work. Payroll should be automatic, accurate, and invisible. If you're stuck fixing tax errors or chasing pay stubs, you're spending energy on the wrong things. The right church payroll software can handle the complexity for you—so you can focus on people, not paperwork.
Here are the three biggest benefits pastors gain when using church payroll software built for ministry:
- More time for pastoral care – Stop wasting hours sorting out payroll errors or manually updating spreadsheets.
- Fewer compliance headaches – No more second-guessing whether you’re handling housing allowance or clergy taxes correctly.
- Clearer oversight with less effort – Know your staff and contractors are paid correctly and legally—without chasing down forms or calculating withholdings by hand.
To get those benefits, look for software that includes:
- Clergy-specific tax handling. Automatically applies dual-status tax rules and housing allowance exemptions so you don’t need to become a tax expert.
- W-2 and 1099 generation. Generates and files tax documents without manual input, cutting out year-end stress and risk.
- Direct deposit with pay scheduling. Pays your team on time without having to log in each cycle or write checks.
- Role-based permissions. Lets admin staff handle day-to-day tasks while keeping sensitive data locked down.
- Self-service employee portals. Gives staff and contractors access to their pay info without you getting involved.
- Error flagging and alerts. Warns you when something looks off—before it causes real problems.
- PTO and time tracking. Lets your team log hours and time off in one place, so you don’t chase down data when payroll is due.
- Automatic tax filing. Sends federal and state forms without you having to touch them.
- Integration with church accounting. Syncs payroll data directly to your general ledger, keeping your books clean.
- Onboarding checklists and templates. Makes it easy to add new hires or pastors without missing required steps.
The best church payroll software doesn’t just “do payroll.” It handles complexity you shouldn’t have to think about—so your focus stays on ministry, not management.
Benefits of Church Payroll Software
Choosing the right church payroll software means freeing your team from time-wasting admin and protecting your organization from compliance slip-ups. For church leaders, finance admins, and anyone juggling operations and ministry, the right system isn’t just helpful—it’s essential.
- Accurate clergy payroll handling. Automates complex tax scenarios like housing allowances and dual-status clergy rules, reducing the risk of IRS penalties.
- Automated tax filing and reporting. Handles quarterly filings, W-2s, and 1099s automatically so no one has to track deadlines or fill out forms by hand.
- Time and PTO tracking in one place. Consolidates staff schedules, time off, and hours worked, making payroll runs smoother and less error-prone.
- Cleaner books through accounting integration. Syncs directly with fund accounting tools so every payroll run is logged and reconciled without double entry.
- Self-service access for staff and contractors. Lets team members view pay stubs, update info, and manage documents without interrupting your day.
Church payroll isn’t a generic HR task—it’s a specialized operational need. Software that’s built for ministry makes the difference between struggling through payday and actually getting to focus on your mission.
Costs & Pricing for Church Payroll Software
Selecting the right church payroll software is crucial for efficient financial management and compliance within your ministry. Understanding the various plan options and their associated costs will help you make an informed decision that aligns with your church's size and needs.
| Plan Type | Average Price | Common Features | Best For |
|---|---|---|---|
| Free Plan | $0/month | Basic payroll processing, employee self-service portal, limited customer support | Small churches with minimal payroll needs |
| Basic Plan | $40/month + $6/employee | Full-service payroll, direct deposit, tax filing, W-2s and 1099s, basic support | Small to medium-sized churches |
| Plus Plan | $80/month + $12/employee | All Basic features, multi-state payroll, next-day direct deposit, time tracking, PTO management | Medium to large churches with growing staff |
| Premium Plan | Custom pricing | All Plus features, dedicated support, HR tools, compliance alerts, advanced reporting | Large churches needing comprehensive HR solutions |
When evaluating these plans, consider your church's size, budget, and specific payroll requirements to choose the most suitable option that ensures compliance and efficiency.
Church Payroll Software Frequently Asked Questions
Can I use church payroll software to pay guest speakers or one-time contractors?
Yes. Most systems support contractor payments, including generating and filing 1099s. Just make sure it allows one-off payments without forcing a recurring pay schedule.
Does church payroll software handle payroll for bi-vocational staff who work part-time at the church?
It should. Good platforms let you set custom pay rates, track part-time hours, and handle clergy-specific tax treatment—even if they only work a few hours a week.
How secure is the employee and financial data stored in the system?
Depends on the provider, but top-tier platforms use encryption, two-factor authentication, and role-based access controls. If those aren’t clearly listed, walk away.
Can I restrict access so only certain staff can view payroll info or run reports?
Yes. Most serious church payroll systems include role-based permissions, so you can control who sees what. Look for customizable access levels, especially if multiple people are managing finances.
What happens if I make a mistake—can I reverse a payroll run or edit a submitted tax form?
Usually. Better platforms offer void or correction tools for payroll runs and amendment workflows for tax filings. But some charge extra for tax re-filings, so check that upfront.
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