Best 11 payroll software for accountants in 2025
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As an accountant, you know that payroll is one of the most critical and complex aspects of your job. From ensuring compliance with changing regulations to managing employee benefits and deductions, there's a lot to keep track of. That's where payroll software comes in.
The right payroll tools can automate repetitive tasks, reduce errors, and free up your time for higher-value work. But with so many options on the market, how do you choose the best fit for your accounting needs?
In this guide, we'll break down the top payroll software for accountants in 2025. We'll cover key features to look for, benefits you can expect, and comparisons of the leading providers. Whether you're a solo practitioner or part of a large accounting firm, you'll come away with actionable insights to streamline your payroll process.
How accountants use payroll software: 4 key tasks
Payroll software has evolved from basic number-crunching to a comprehensive tool for managing the entire employee payment process. Here are some of the core tasks accountants perform using payroll solutions:
1. Set up payroll schedules for employees and contractors
One of the first steps in any payroll process is establishing pay schedules. Will employees be paid weekly, bi-weekly, semi-monthly or monthly? What about contractors or freelancers? Payroll software allows you to configure these details for each worker, ensuring timely and accurate payments. You can also easily make adjustments as needed, such as adding a new hire or switching someone from salary to hourly.
2. Manage tax compliance
Payroll tax laws are notoriously complex, with requirements varying by state. Keeping up with filing deadlines, calculating withholdings, and issuing W-2s and 1099s can be a full-time job in itself. The best payroll software takes much of this burden off your plate. It automatically applies the latest federal, state, and local tax rates to each paycheck. It reminds you of upcoming filing due dates. And it generates year-end forms for employees and contractors. That peace of mind is priceless.
3. Automate bookkeeping entries for payroll expenses and liabilities
Every payroll run impacts your books, from recording wages paid to tracking tax liabilities and benefit deductions. Manually entering this data into your accounting system is tedious and error-prone. With payroll software, those entries can be automated. Each pay run syncs seamlessly with your general ledger, posting expenses and liabilities to the right accounts. You can also easily export payroll data for deeper analysis in your preferred reporting tool.
4. Track employee benefits and deductions
Health insurance, retirement plans, HSA contributions—employee benefits are a key piece of total compensation. But administering those benefits through payroll can get complicated fast. Payroll software simplifies the process by automatically calculating and applying employee deductions each pay period. You can easily track employer contributions, catch enrollment changes, and keep tabs on eligibility and compliance.
3 benefits of payroll software for accountants
We've seen how payroll software supports key accounting tasks and responsibilities. But what's the bigger picture value? Here are three high-level benefits you can expect:
1. Enhanced compliance and accuracy
Payroll mistakes can be costly, from tax penalties to employee lawsuits. The best payroll solutions have compliance guardrails built in, from automated tax calculations to I-9 and W-4 verification. They're constantly updating to reflect the latest laws and regulations. And they're run through rigorous testing to ensure the numbers are right, every time. That means you can run payroll with confidence, knowing that compliance is virtually guaranteed.
2. Improved efficiency through automation
Time is money, and payroll can be a major time sink. For accountants juggling dozens of clients, that adds up fast. Payroll software automates the most repetitive and manual aspects of payroll processing. Think data entry, tax calculations, report generation, and more. Those efficiency gains free you up to focus on more strategic and revenue-driving activities, like financial planning and analysis. It's a win-win for you and your clients.
3. Better finance management
With the right software, you can easily track labor costs, forecast future expenses, and spot trends and anomalies. You can slice and dice data by department, location, or job type. And you can quickly generate custom payroll reports to answer ad hoc questions. In short, payroll software gives you the insights you need to be a true strategic partner. You can help your clients make smarter decisions about hiring, compensation, and more.
Best 11 payroll software for accountants in 2025
Looking for some of the best payroll platforms out there? Here’s our carefully curated list:
1. Rippling
Rippling offers a comprehensive, unified platform that combines HR, IT, and finance systems into one integrated solution. The system leverages its unified employee database to automatically sync payroll with benefits, time tracking, and expense management, eliminating manual work and reducing human error across all processes. Rippling is built in-house with all modules natively integrated, unlike competitors who often rely on third-party acquisitions.
Key features
Automated tax calculations and filings across all 50 states
Pay run comparison tool to track changes between payrolls
Unlimited off-cycle payroll runs at no extra charge
Custom pay types for bonuses, tips, and recurring payments
Paperless W-2, W-4, and 1099 processing
Multiple pay rates and retroactive pay support
Garnishment management
Global payroll capabilities for international teams
Pros
Automated compliance monitoring and alerts
Higher rated user experience
Native integrations with QuickBooks, Xero, and NetSuite
Seamless integration between all modules
Granular permissions control for payroll approvals
Mobile app for on-the-go payroll management
2. ADP RUN
ADP's small business solution offers payroll and HR functionality for companies with simpler needs.
Key features
Federal, state, and local tax filing
Mobile payroll services
Employee self-service portal
Pros
Wide network of tax compliance expertise
Strong mobile app functionality
Customizable payroll reports
3. QuickBooks Payroll
QuickBooks Payroll is Intuit's payroll solution that focuses on providing payroll processing for accountants and businesses already using QuickBooks for their needs.
Key features
Same-day direct deposit
Automated tax calculations
Mobile payroll management
Pros
Smooth QuickBooks integration
Tax penalty protection
Automated payroll options
4. Xero
Xero is a cloud-based accounting software with integrated payroll capabilities focused on small businesses. The platform emphasizes the connection between accounting and payroll functions to create a more streamlined workflow.
Key features
Integrated accounting and payroll
Multiple user access levels
Automated tax calculations
Pros
Strong accounting integration
Employee self-service through mobile app
Detailed reporting tools
5. Paylocity
Paylocity is a web-based payroll and HR platform serving businesses of all sizes.
Key features
Customizable payroll workflows
Integrated time and attendance
Employee self-service portal
Pros
Learning management system (LMS) for employee training
Extensive reporting capabilities
Automated tax management
6. Gusto
Gusto is a payroll platform that combines essential payroll functions with basic HR tools to provide a complete solution for smaller organizations.
Key features
Automated tax filings
Benefits administration
Time tracking integration
Pros
Built-in benefits management
Transparent pricing structure
Employee self-service
7. OnPay
OnPay provides payroll, HR and benefits capabilities that allows accountants to run their practice more efficiently.
Key features
Unlimited payroll runs
Multi-state payroll processing
Automated tax filings
Pros
Transparent pricing
Free payroll setup assistance
Integrated HR tools
8. Workday
Workday is an enterprise-level HCM platform providing payroll capabilities for larger organizations. The system is designed to handle complex payroll needs while integrating with broader HR and financial management functions.
Key features
Global payroll processing
Real-time analytics
Continuous payroll processing
Pros
Strong enterprise features
Built-in compliance tools
Advanced reporting capabilities
9. Patriot
Patriot is a payroll software that provides essential payroll functions while offering free setup assistance and US-based support.
Key features
Free direct deposit
Time-off accruals tracking
Customizable deductions
Pros
Free co-branding
Discounted pricing
Consolidated billing
10. Deel
Deel is a global payroll platform specializing in international workforce management and contractor payments.
Key features
Global contractor payments
Automated invoice generation
Multi-currency support
Pros
Strong international compliance
Built-in payment options
Automated tax documentation
11. Paychex
Paychex is another online payroll and HR software solution designed for businesses of all sizes.
Key features
Benefits management
Compliance tools
HR services
Pros
Flexible payment options
Customizable dashboard
Integrated time tracking
Best 3 payroll and accounting software for small business
Among these providers, here are the top three solutions specifically optimized for small business payroll and accounting needs:
1. Rippling
Rippling offers a comprehensive solution that combines payroll, HR, and IT management, making it particularly suitable for growing small businesses. The platform scales seamlessly as businesses expand, handling everything from basic payroll needs to complex multi-state operations. While it offers enterprise-level capabilities, its intuitive interface and automation features make it accessible for small business users.
Key features
Automated tax filing and compliance
Built-in time and attendance tracking
Employee self-service portal
Integration with 600+ business applications
Customizable workflow automation
Full benefits administration
2. Gusto
Gusto is a payroll platform designed for small businesses seeking simplicity in their payroll processes. The platform offers a straightforward approach to payroll with built-in time tracking and benefits administration, allowing businesses to manage everything easily.
Key features
Unlimited payroll runs
Integrated time tracking
Benefits administration
Employee self-service
3. Deel
Deel is a global payroll platform that makes it easy for small businesses to handle both domestic and international payroll. The platform provides US payroll processing in all 50 states while offering international payment capabilities.
Key features
US and global payroll processing
Benefits administration
Compliance monitoring
Multi-currency support
How to choose the best payroll software for accountants: 4 features
With so many payroll options out there, how do you narrow down the choices? Here are four key features to prioritize in your evaluation process:
1. Integrations with accounting software
If you're managing payroll for multiple clients, you need a system that plays nicely with your existing accounting tools. Look for payroll software with pre-built integrations with popular platforms like QuickBooks, Xero, and FreshBooks. The best integrations will automatically sync payroll data with your general ledger, eliminating manual entry and ensuring consistency. Bonus points for real-time sync that gives you up-to-the-minute financial visibility.
2. Tax filing and compliance support
Staying on top of payroll tax requirements is one of the biggest challenges for accountants. The best payroll software will have built-in safeguards to ensure compliance at the federal, state, and local levels. Look for features like automatic tax calculations, quarterly and annual filing deadlines, and year-end tax form generation for employees and contractors. Some providers will even handle tax payments and filings on your behalf, giving you even greater peace of mind.
3. Employee self-service options
Payroll isn't just about numbers, it's about people. And giving employees some self-service capabilities can drastically cut down on your administrative workload. At a minimum, employees should be able to view pay stubs and update personal information like bank account details. More advanced employee portals may also include features like time-off requests, document uploads, and benefits enrollment. By empowering employees to manage some of their own payroll tasks, you can focus on higher-level client work.
4. Scalability and customization
Your clients' payroll needs will evolve over time, and your software should be able to keep up. Look for a system that can accommodate different types of workers, pay schedules, and benefits packages. The ability to create custom pay types, deductions, and reports can also be invaluable for handling unique client scenarios. And if you work with larger clients, consider providers that offer advanced features like multi-state payroll, job costing, and labor distribution.
Rippling: Streamline payroll for your accountants
While there are many excellent payroll solutions on the market, Rippling stands out for its unique combination of power and flexibility. Its unified employee database and customizable workflows can save you hours of manual effort each month.
Rippling's platform automates everything from tax calculations and year-end forms to custom pay runs and approval flows, all while integrating seamlessly with your existing accounting and financial reporting tools. The system's unified approach means your payroll data automatically syncs with benefits, time tracking, and expense management, eliminating manual work and reducing the risk of errors.
As your practice grows, Rippling scales effortlessly to support larger clients with advanced payroll needs, while maintaining the same intuitive interface and automated workflows that make it efficient for smaller organizations. With industry-leading support response times, you can trust Rippling to handle your clients' most complex payroll requirements.
If you're ready to see how Rippling can streamline your payroll process, sign up for a free demo today. You'll get a personalized walk-through of the platform and see firsthand how it can support your accounting practice.
FAQs on the best payroll software for accountants
What are the best practices for payroll accountants?
Some key best practices include:
Staying up-to-date on the latest tax laws and regulations
Establishing clear processes and approval workflows for payroll tasks
Reconciling payroll data with bank statements and financial reports regularly
Keeping detailed records and documentation for auditing purposes
Communicating proactively with clients about payroll deadlines and requirements
Using payroll software that automates repetitive tasks and ensures compliance can make it much easier to implement these best practices consistently.
Is payroll software suitable for accounting firms managing multiple clients?
Absolutely. In fact, payroll software is especially valuable for accountants juggling multiple client accounts. The right payroll software can help you efficiently manage payroll for dozens or even hundreds of clients, without sacrificing accuracy or compliance.
Can payroll software handle international payroll for accountants with global clients?
It depends on the specific software, but some payroll solutions do offer international capabilities. Rippling, for example, supports payroll processing in over 185 countries. If you have clients with global teams, look for features like multi-currency support and exchange rate tracking, compliance with local tax laws and regulations, integrations with global payment providers and banks, localized employee self-service portals and support, and consolidated reporting across international entities. Keep in mind that international payroll can be very complex, so it's important to thoroughly vet any software provider's global capabilities before committing.
Why should accountants choose Rippling over other payroll software?
Rippling offers a unique combination of automation, customization, and integration that sets it apart from other payroll solutions. Some of the key advantages include:
A unified database that syncs employee data across payroll, HR, IT
Highly customizable approval flows and pay run configurations
Robust reporting and analytics to support strategic advising
Seamless integration with accounting, time tracking, and expense management tools
Global payroll capabilities to support clients with international teams, and
Dedicated support from payroll experts and accounting professionals.
But ultimately, the best way to see if Rippling is right for your practice is to try it out yourself. Sign up for a free demo today and experience the difference firsthand.
Disclaimer
Rippling and its affiliates do not provide tax, accounting, or legal advice. This material has been prepared for informational purposes only, and is not intended to provide or be relied on for tax, accounting, or legal advice. You should consult your own tax, accounting, and legal advisors before engaging in any related activities or transactions.
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The Rippling Team
Global HR, IT, and Finance know-how directly from the Rippling team.
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