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10 Best Payroll Software for Accountants
By Jodie Price | Updated November 10, 2025
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OnPay
Recognized as “Best for Accountant Support,” OnPay starts at $40 per month plus $6 per person. It provides automatic payroll tax filing and allows unlimited payroll runs, offering a streamlined solution for firms handling numerous clients.
Expert Take
OnPay simplifies payroll by allowing unlimited monthly runs at no extra cost while managing tax filings at the federal, state, and local levels. It supports both W-2 employees and 1099 contractors and integrates with QuickBooks and Xero, keeping payroll and accounting data synchronized for better accuracy and efficiency.
Beyond payroll, OnPay offers HR tools for onboarding, compliance, and benefits management. Its Partner Program enhances value with free firm payroll, marketing support, and revenue-sharing opportunities. Designed for small to mid-sized businesses, OnPay delivers robust, transparent, and affordable payroll and HR solutions without hidden fees.
Pros & Cons
Pros
- Unlimited payroll runs with no extra charges
- Automated tax filing and payments
- Supports both W-2 employees and 1099 contractors
- Integrates with QuickBooks and Xero for accounting sync
- Includes HR tools like onboarding and compliance support
Cons
- Limited global payroll support (U.S.-focused)
- Fewer advanced reporting options compared to larger platforms
- Benefit options may depend on state availability
- No dedicated mobile app for employees, only mobile-friendly access
Specs
Feature Details Self-Service Employee Portal Yes; Employees can view pay stubs, tax forms, and update personal details online Next-Day Direct Deposit No Automated Tax Payments Yes; Federal, state, and local payroll taxes calculated, filed, and paid automatically Compliance Assistance Yes; Tools and reminders help meet labor law and tax compliance requirements New-Hire Onboarding Yes; Digital onboarding with e-signatures, document collection, and setup guidance -
Rippling
Labeled as “Best for Automated Payroll Processing,” Rippling starts at $35 per month plus $8 per user. It includes automatic payroll tax filing and supports unlimited payroll runs, making it a reliable option for businesses that prioritize efficiency and accuracy.
Expert Take
Rippling streamlines payroll by automating calculations, syncing employee data, and minimizing manual entry errors. It integrates payroll with HR tools like onboarding, benefits, and time tracking, allowing businesses to manage operations from one dashboard. For accountants, this reduces administrative tasks and ensures faster, more accurate payroll processing.
Its vast integration network connects payroll with accounting, expense management, and performance tools, making it ideal for project-based or global teams. Customizable workflows handle bonuses and retroactive adjustments, while granular access controls protect sensitive data. Combined with automated tax filings, Rippling delivers accuracy, flexibility, and compliance in one cohesive platform.
Pros & Cons
Pros
- Supports both U.S. and global payroll
- Integrates payroll with HR, benefits, and time tracking
- Automated tax filing and payments
- User-friendly setup and dashboard
- Scales well for growing businesses
Cons
- Pricing is not fully transparent without a quote
- May include more HR features than needed if only payroll is required
- Some advanced tools require add-ons, increasing overall cost
- Limited offline support options compared to larger providers
Specs
Feature Details Self-Service Employee Portal Yes; Employees can access pay stubs, tax forms, and personal info updates Next-Day Direct Deposit No Automated Tax Payments Yes; Federal, state, and local payroll taxes are calculated, filed, and paid automatically Compliance Assistance Yes; Built-in tools help ensure payroll follows labor laws and tax regulations New-Hire Onboarding Yes; Digital workflows handle paperwork, tax forms, and benefits enrollment for new employees -
Justworks
Recognized as “Best for Client Management,” Justworks starts at $50 per month plus $8 per person. It offers automatic payroll tax filing and unlimited payroll runs, making it a strong choice for firms that want both efficiency and scalability in managing clients.
Expert Take
Justworks blends payroll software with professional employer organization (PEO) services, offering automated payroll, tax filing, benefits administration, and compliance tools in one platform. Its unified sign-in and detailed permissions allow accountants and businesses to manage client data efficiently, reduce administrative tasks, and keep HR and payroll in sync.
The Advisor Dashboard provides accountants with expert support and streamlined client management, though its third-party integrations are more limited than some competitors. With flexible PEO plans that scale from core payroll to advanced analytics, Justworks is ideal for firms seeking an all-in-one payroll, HR, and compliance solution.
Pros & Cons
Pros
- Automates payroll and tax filings
- Offers access to health, dental, and vision benefits
- Compliance support helps reduce legal risks
- Easy onboarding for new hires
- 24/7 customer support
Cons
- Higher cost compared to payroll-only software
- Limited customization for advanced payroll needs
- Some features locked behind PEO plans
- Not the best fit if you only want basic payroll
Specs
Feature Details Self-Service Employee Portal Yes; Employees can view pay stubs, update personal info, and access benefits online Next-Day Direct Deposit No Automated Tax Payments Yes; Federal, state, and local payroll taxes are calculated, filed, and paid automatically Compliance Assistance Yes; Helps you stay compliant with labor laws, ACA, and other regulations New-Hire Onboarding Yes; Digital onboarding lets new employees complete paperwork and enroll in benefits online -
Gusto
Labeled as “Best Accountant Dashboard,” Gusto starts at $40 per month plus $6 per person. It provides automatic payroll tax filing and unlimited payroll runs, making it a reliable solution for accountants seeking both efficiency and ease of use.
Expert Take
Gusto automates payroll and tax filings at every level while offering fast direct deposits and a self-service employee portal for managing pay stubs and tax forms. Its digital onboarding tools streamline hiring by allowing new employees to complete paperwork and set up direct deposits electronically, keeping records organized from day one.
For accountants, Gusto Pro offers alerts on compliance updates, workforce changes, and client savings opportunities. Its People Analytics tracks retention and payroll trends, while the partner program provides free payroll, revenue sharing, and HR support. With built-in compliance tools and advisory resources, Gusto helps firms manage payroll efficiently and grow client relationships.
Pros & Cons
Pros:
- Automated payroll tax filing at all levels
- Easy-to-use dashboard with clear navigation
- Employee self-service reduces admin work
- Next-day direct deposit available on most plans
- Built-in onboarding tools for new hires
Cons:
- Limited scalability for larger enterprises
- Customer support response times can vary
- Some advanced HR features cost extra
- Not as customizable as enterprise payroll systems
Specs
Feature Details Self-Service Employee Portal Yes; Employees can access pay stubs, W-2s, and update personal information Next-Day Direct Deposit Yes; Available with most subscription tiers; speeds up payroll delivery Automated Tax Payments Yes; Handles federal, state, and local tax filings and payments automatically Compliance Assistance Yes; Provides reminders and tools for labor law and tax compliance New-Hire Onboarding Yes; Digital onboarding with e-signatures, direct deposit setup, and form I-9 -
Remote
Recognized as “Best for Global Accountants,” Remote starts at $29 per employee. It includes automatic payroll tax filing but does not offer unlimited payroll runs, making it a practical choice for firms managing international teams with straightforward payroll needs.
Expert Take
Remote helps businesses manage global teams by combining payroll, compliance, and HR into one platform. It handles local labor laws, tax rules, and benefits in multiple countries, ensuring compliance and reducing risk. This makes managing international payroll as seamless as domestic operations, ideal for globally distributed workforces.
Its Global Employment Country Selector guides companies in choosing where to hire based on cost, talent, and time zones. Remote also offers employer of record (EOR) services for large enterprises and all-in-one HR tools for smaller firms. Though pricing is higher than U.S.-only options, it delivers unmatched efficiency for international operations.
Pros & Cons
Pros:
- Supports payroll in multiple countries
- Built-in compliance with local regulations
- Automates tax filing and payments
- Provides tools for onboarding new hires
- Offers employee self-service features
Cons:
- Higher cost than many U.S.-only payroll tools
- May feel complex if you only hire in one country
- Limited customization compared to some accounting-focused platforms
- Customer support response times can vary
Specs
Feature Details Self-Service Employee Portal Yes; Employees can view pay stubs, update personal info, and access tax forms Next-Day Direct Deposit Not offered Automated Tax Payments Yes; Calculates and files taxes in each supported country automatically Compliance Assistance Yes; Monitors labor laws, benefits, and contracts to ensure legal compliance New-Hire Onboarding Yes; Provides digital contracts, document collection, and setup for payroll -
Workful
Labeled as “Best for Accountant Collaboration,” Workful starts at $45 plus $7 per person. Unlike some competitors, it does not include automatic payroll tax filing or unlimited payroll runs, making it more suited for firms that prioritize collaboration features over automation.
Expert Take
Workful simplifies payroll management by enabling accountants and payroll professionals to collaborate efficiently on client accounts. It integrates with QuickBooks Online, time tracking, and expense reporting, keeping payroll data synchronized. Shared access controls and centralized billing make managing multiple clients organized and efficient.
The platform offers clear, affordable pricing with features like automated overtime tracking, PTO management, and mileage reimbursement. It generates key payroll reports, including tax liabilities and timesheets, making compliance straightforward. While it lacks advanced analytics, Workful provides small businesses with an affordable, easy-to-use payroll and HR solution.
Pros & Cons
Pros:
- Easy payroll setup with automated tax filing
- Employee self-service portal reduces administrative workload
- Next-day direct deposit available for faster payments
- Built-in compliance support for tax regulations
- Onboarding tools for new employees
Cons:
- Limited integrations with third-party apps
- Reporting features are less detailed than larger platforms
- Not as scalable for very large teams
- Fewer advanced HR tools compared to competitors
Specs
Feature Details Self-Service Employee Portal Yes; Employees can view pay stubs, update personal info, and access tax forms Next-Day Direct Deposit Not offered Automated Tax Payments Not offered Compliance Assistance Yes; Built-in tools to stay aligned with payroll tax rules and deadlines New-Hire Onboarding Yes; Digital setup for W-4, I-9, and payroll details during employee hiring -
QuickBooks Payroll
Positioned as “Best for QuickBooks Clients,” QuickBooks Payroll starts at $50 plus $6 per person. It includes automatic payroll tax filing and unlimited payroll runs, making it a strong choice for firms already using QuickBooks for accounting.
Expert Take
QuickBooks Payroll integrates seamlessly with QuickBooks accounting, allowing businesses to manage payroll and bookkeeping from a single platform. It automates tax calculations and filings, supports direct deposit, and simplifies employee onboarding, making payroll management faster, more accurate, and fully compliant for accountants and business owners alike.
While its cost can increase with additional features and more employees, QuickBooks Payroll delivers strong automation and convenience. It is best suited for small to midsize businesses seeking a unified system for payroll and accounting, minimizing manual work while keeping financial records organized.
Pros & Cons
Pros:
- Seamless integration with QuickBooks accounting
- Automated tax filing and payment
- Next-day direct deposit available
- Easy employee onboarding tools
- Compliance support for payroll regulations
Cons:
- Pricing increases with more employees
- Limited customization compared to larger providers
- Some advanced HR features require higher-tier plans
- Customer support may not always be consistent
Specs
Feature Details Self-Service Employee Portal Yes; Employees can view pay stubs, W-2s, and update personal details online. Next-Day Direct Deposit Yes; Pay employees as soon as the next business day at no extra cost. Automated Tax Payments Yes; Calculates, files, and pays federal and state payroll taxes automatically (Premium and Elite plans only). Compliance Assistance Yes; Provides tools to meet payroll tax rules and alerts for changes in regulations. New-Hire Onboarding Yes; Through third-party HR service; allows digital setup of employee information and e-signature collection. -
Wave Payroll
Labeled as “Best for Integrated Payroll and Accounting Software,” Wave Payroll starts at $20 plus $6 per person. Automatic payroll tax filing is available only in 14 states, and the platform does not support unlimited payroll runs, making it more suitable for smaller teams in supported regions.
Expert Take
Wave simplifies payroll by integrating seamlessly with its accounting software, offering small businesses an all-in-one solution for payroll, invoicing, and expense tracking. It supports direct deposit, employee self-service, and compliance features, making it easy to manage financial operations and employee payments in one platform.
Payroll tax filings are automated in select states, though manual filing is required elsewhere. While it lacks advanced HR features, Wave’s affordability and integration with Wave Accounting make it ideal for startups and small businesses seeking simplicity over complex, enterprise-level functionality.
Pros & Cons
Pros:
- Integrates with Wave Accounting for seamless bookkeeping
- Easy to set up and use for small teams
- Employee self-service portal reduces admin tasks
- Next-day direct deposit available in many states
- Affordable compared to larger payroll platforms
Cons:
- Limited tax filing support outside certain states
- No advanced HR tools such as benefits management
- Lacks scalability for growing businesses
- Customer support options are not as extensive as larger providers
- Fewer integrations beyond Wave’s own ecosystem
Specs
Feature Details Self-Service Employee Portal Yes; Employees can view pay stubs, update personal details, and access tax forms. Next-Day Direct Deposit Not offered Automated Tax Payments Yes, but only in 14 states; full-service tax filing only in select states; manual filing required elsewhere. Compliance Assistance Not offered New-Hire Onboarding Not offered -
ADP RUN
Labeled as “Best for Accountant Marketing,” ADP RUN does not list a starting monthly price but provides automatic payroll tax filing to streamline compliance. It also supports unlimited payroll runs, making it a flexible option for firms managing frequent or complex payroll schedules.
Expert Take
ADP RUN automates payroll by calculating wages, managing tax withholdings, and handling filings to reduce errors and save time. It supports next-day direct deposit and provides employees with a self-service portal for viewing pay stubs and managing personal details, improving efficiency for both employers and staff.
Beyond payroll, ADP RUN integrates with accounting software like QuickBooks and Xero to keep financial data in sync. Built-in compliance tools help businesses stay aligned with tax laws and labor regulations, making it a reliable choice for small and midsize companies seeking an all-in-one payroll and HR solution.
Pros & Cons
Pros:
- Easy-to-use interface for small business owners
- Automated tax filing and payment included
- Next-day direct deposit option available
- Employee self-service portal reduces administrative tasks
- Strong compliance support and reporting tools
- Integration with accounting systems like QuickBooks
Cons:
- Pricing is not transparent and requires a quote
- Extra fees for some add-ons, such as HR tools
- May be more than you need if you have very few employees
- Limited customization compared to larger enterprise systems
Specs
Feature Details Self-Service Employee Portal Yes; Employees can access pay stubs, W-2 forms, and update personal details. Next-Day Direct Deposit Yes; Available for faster employee payments. Automated Tax Payments Yes; Calculates, withholds, and files federal, state, and local payroll taxes. Compliance Assistance Yes; Helps maintain compliance with labor laws and tax regulations. New-Hire Onboarding Yes; Allows digital collection of employee forms and basic onboarding steps. -
Square Payroll
Positioned as “Best for Simple Invoicing,” Square Payroll starts at $35 plus $6 per person and includes automatic payroll tax filing. It also supports unlimited payroll runs, making it a practical option for businesses that need both affordability and straightforward payroll processing.
Expert Take
Square Payroll automates wage calculations, tax withholdings, and deductions while filing federal and state payroll taxes on your behalf. It supports both W-2 employees and 1099 contractors, syncing hours directly from Square’s time-tracking system to ensure accuracy and reduce manual entry.
Though limited in advanced HR and international features, Square Payroll remains affordable and user-friendly. It’s ideal for small to midsize U.S. businesses, particularly those using Square for point-of-sale, seeking a reliable, streamlined payroll solution that simplifies compliance and saves time.
Pros & Cons
Pros:
- Easy setup and clean interface
- Automatic tax filing and payments
- Integrates with Square POS and time tracking
- Supports both employees and contractors
- Affordable flat-rate pricing
Cons:
- Limited global payroll support
- Fewer HR features compared to full-service platforms
- No advanced reporting customization
- Customer support response can be slower during peak times
Specs
Feature Details Self-Service Employee Portal Employees can view pay stubs, update details, and access tax forms online. Next-Day Direct Deposit Funds reach employee bank accounts as soon as the next business day. Automated Tax Payments Federal and state payroll taxes are filed and paid automatically. Compliance Assistance Helps you stay aligned with labor laws and payroll regulations. New-Hire Onboarding Lets you add new employees, collect forms, and set up direct deposit digitally.
Frequently Asked Questions
What features should accountants look for in payroll software to efficiently manage multiple clients?
Accountants should look for multi-client dashboards, automated tax filing, and bulk processing tools. Strong reporting capabilities, secure data storage, and compliance tracking are also essential. Cloud access allows management of client accounts from anywhere without switching between systems.
What is payroll software for accountants?
Payroll software for accountants automates payroll processing and integrates it with other financial services. It tracks employee compensation, labor costs, and compliance with payroll and workforce regulations at the federal, state, and local levels, helping firms manage clients’ payroll operations more efficiently.
What pretax deductions are supported by payroll software for accountants?
Payroll software can handle pretax deductions such as retirement plan contributions, health and life insurance premiums, commuter benefits, and health or flexible spending accounts (HSA/FSA). These deductions lower taxable income, reducing the amount withheld for federal and state income taxes.
How do employees benefit from payroll software for accountants?
Employees gain convenient access to pay records and benefits through online portals or mobile apps, where they can update personal information and manage benefits. Many platforms also support onboarding, time tracking, and training, simplifying HR processes for both employers and staff.
How can accountants identify the right payroll software for their practice?
The right payroll software should streamline every step of payroll management, from tax calculations to reporting, while ensuring compliance. Accountants should prioritize platforms that integrate seamlessly with their workflow, minimize manual data entry, and offer advanced features for managing multiple clients effectively.