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Whether you're an accountant at a small firm or a CPA managing multiple clients, the right payroll software can make a significant difference in your workflow. Payroll software can save you time and headaches by automating wage calculations and distribution, ensuring compliance with tax regulations, and reducing errors along the way.

Yet with so many options out there, choosing the right payroll software for accounting can be overwhelming with. With years of experience using, testing, and reviewing various accounting software, here are my top picks for the best payroll software for accounting:

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Best Payroll Software for Accountants Software Summary

This comparison chart summarizes pricing details for my top payroll software selections for accountants to help you find the best software for your budget and business needs.

Tools Price
FreshBooks From $19/per/month
Gusto From $6/user/month + $40 base fee (billed annually)
Paycom Pricing upon request
Wagepoint From $4/employee/month + $20/month
Patriot Payroll From $4/employee/month + $17/month base fee
Accounting CS Payroll Pricing upon request
Justworks Payroll From $8/employee/month + $50/month base fee
Deel Flat rate user pricing, with a free version for businesses with up to 200 people
Xero From $14.50/user/month
Papaya Global From $15/employee/month
Preview Image - <h2 class="c-block__title b-summary-table__title c-listicle__title h3" > Compare Software Specs Side by Side</h2>

Compare Software Specs Side by Side

Use our comparison chart to review and evaluate software specs side-by-side.

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How To Choose Payroll Software for Accountants

As you work through your own unique software selection process, keep the following points in mind:

  • Integration with Existing Systems: Ensure the payroll software integrates seamlessly with your current accounting and HR systems. This is crucial for maintaining data consistency and streamlining operations. For example, if your firm uses QuickBooks for accounting, choosing a payroll solution that integrates with QuickBooks can save time and reduce errors by eliminating the need for manual data entry.
  • Tax Compliance and Automation: The software should handle tax calculations, withholdings, and filings automatically. This feature is essential to avoid costly mistakes and ensure compliance with federal, state, and local tax regulations. For instance, Gusto offers automated tax filing and compliance updates, which can be a significant time-saver and reduce the risk of penalties.
  • User-Friendly Interface: A user-friendly interface is vital for efficient operation. The software should be easy to navigate for both accountants and employees. Features like self-service portals where employees can access their pay stubs and tax documents can reduce the administrative burden on your team. Namely, for example, provides a self-service portal that allows employees to manage their own payroll information, which can enhance user experience and efficiency.
  • Scalability and Flexibility: Choose a payroll solution that can grow with your business. It should be able to handle an increasing number of employees and adapt to changing business needs. For example, OnPay offers scalable solutions that can accommodate businesses of various sizes, making it a good choice for firms that anticipate growth.
  • Customer Support and Reviews: Reliable customer support is crucial for resolving issues quickly and effectively. Look for software with positive reviews regarding customer service. Sites like G2 and Capterra can provide insights into user experiences. For instance, Paychex Flex is known for its helpful customer support, which can be a critical factor when dealing with complex payroll issues.

Best Payroll Software For Accountants Reviews

This in-depth analysis provides overviews of various payroll software options for accountants. I will walk through the pros and cons of each tool, their features, and their best use cases.

Best for user-friendly invoicing and expense tracking

  • 30-day free trial
  • From $19/per/month
Visit Website
Rating: 4.5/5

FreshBooks is a comprehensive accounting software designed for small businesses. It offers invoicing, expense tracking, and payroll services.

Why I picked FreshBooks:

I chose FreshBooks for its exceptional ease of use and comprehensive feature set. FreshBooks stands out for its user-friendly design, which simplifies invoicing and expense tracking, making it ideal for small business owners. Its integration with Gusto for payroll services further enhances its utility and makes it a great duo for payroll and accounting features. 

Standout features & integrations:

Features include automated invoicing, expense tracking, time tracking, and project management. It also includes payroll services powered by Gusto, which offers automatic tax filings and direct deposits.

Integrations include over 100 tools, including Gusto, Stripe, PayPal, Shopify, G Suite, Slack, Trello, HubSpot, Mailchimp, and Zapier.

Pros and cons


  • Strong integration options
  • Intuitive invoicing features
  • User-friendly interface


  • Limited advanced features
  • Higher cost for additional users

Best for comprehensive payroll and HR solutions

  • Free demo available
  • From $6/user/month + $40 base fee (billed annually)
Visit Website
Rating: 4.3/5

Gusto offers a comprehensive suite of payroll and HR solutions designed to streamline business operations. It provides automated payroll, tax filing, and HR services, making it an all-in-one platform for managing employee-related tasks.

Why I picked Gusto:

I chose Gusto for its power duo of payroll and HR features, which stand out in the market of payroll software with accounting features. Gusto's ability to handle everything from payroll to employee benefits and compliance makes it a versatile tool for businesses of all sizes. It is best for comprehensive payroll and HR solutions because it integrates payroll, benefits, and HR functionalities into a single platform, ensuring seamless management of employee data and compliance.

Standout features & integrations:

Features include automated payroll processing, tax filing, employee benefits management, and compliance tracking. It also offers tools for hiring and onboarding, time tracking, and performance management.

Integrations include QuickBooks, Xero, FreshBooks, TSheets, Expensify, When I Work, Deputy, Clover, G Suite, and Slack.

Pros and cons


  • Employee benefits management
  • Automated tax filing
  • Comprehensive HR and payroll features


  • Limited international payroll support
  • Higher starting price

Best for scalable HR and payroll software

  • Free demo available
  • Pricing upon request

Paycom offers flexible and scalable HR and payroll software that streamlines everyday business tasks. It provides seamless and secure connections to client data, allowing for unparalleled efficiency and synergy in delivering customer care.

Why I picked Paycom:

I chose Paycom for its comprehensive approach to HR and payroll, which stands out in the crowded market of payroll software. Its scalability and efficiency make it ideal for growing businesses and accounting firms. I believe Paycom is best for scalable HR and payroll software because it offers a single platform that integrates various HR functions, making it easier to manage and expand as business needs grow.

Standout features & integrations:

Features include GL Concierge for tracking payroll accounting data, Labor Allocation for detailed workforce planning, Report Center for generating real-time reports, and Direct Data Exchange® for monitoring HR tech usage.

Integrations include QuickBooks, Xero, NetSuite, Microsoft Dynamics, Sage, ADP, Kronos, Workday, Oracle, and SAP.

Pros and cons


  • Real-time reporting
  • Scalable for growth
  • Comprehensive HR features


  • Complex setup
  • Pricing upon request

Best for automating payroll processing

  • Free trial available
  • From $4/employee/month + $20/month

Wagepoint is a payroll software designed to simplify and automate payroll processing for accountants and bookkeepers. It offers a range of features to ensure accurate and efficient payroll management.

Why I picked Wagepoint:

I chose Wagepoint for its automation capabilities that significantly reduce the time and effort required for payroll processing. Its focus on simplicity and efficiency makes it stand out from other payroll software. I believe Wagepoint is best for automating payroll processing due to its ability to handle complex payroll tasks seamlessly, ensuring compliance and accuracy.

Standout features & integrations:

Features include automated payroll tax remittances, year-end tax documents, and a convenient online employee portal for pay stubs and tax documents. 

Integrations include QuickBooks, Xero, FreshBooks, Gusto, JustWorks, Patriot Payroll, Paycom, Papaya Global, Deel, and OnPay.

Pros and cons


  • Built to handle complex payroll tasks
  • Automated tax filings
  • Easy to use


  • Higher cost for small teams
  • Limited customization

Best for affordable payroll with USA-based support

  • 30-day free trial
  • From $4/employee/month + $17/month base fee

Patriot Payroll is an affordable and customizable payroll platform designed for small businesses. It offers features such as customizable deductions and contributions, printable W-2s, a free employee portal, time-off accruals, multiple pay rates, and a net-to-gross payroll tool.

Why I picked Patriot Payroll:

I chose Patriot Payroll for its affordability and USA-based support, which makes it stand out from other payroll software. The combination of low pricing and dedicated customer service ensures that small businesses get the help they need without breaking the bank. I believe it is best for affordable payroll because it offers comprehensive features at a lower cost compared to competitors, along with reliable support.

Standout features & integrations:

Features include customizable deductions, printable W-2s, a free employee portal, time-off accruals, multiple pay rates, and a net-to-gross payroll tool. The software also provides accurate payroll and tax calculations, free direct deposit, and automated time-off accruals.

Integrations include QuickBooks, Xero, TSheets, QuickBooks Time, Deputy, Gusto, FreshBooks, Expensify, When I Work, and G Suite.

Pros and cons


  • Customizable payroll options
  • USA-based support
  • Affordable pricing


  • Additional state filing fees
  • Limited to USA companies

Best for batch-oriented payroll calculations

  • Pricing upon request

Accounting CS Payroll is designed to streamline payroll processes for accounting professionals. It offers advanced solutions for time entry, paycheck delivery, and more. It stands out due to its ability to perform payroll calculations quickly and efficiently.

Why I picked Accounting CS Payroll:

I chose Accounting CS Payroll for its quick and handy batch-oriented payroll processing capabilities. This tool stands out because it allows accountants to handle multiple clients' payrolls simultaneously, significantly increasing efficiency. I believe it is best for batch-oriented payroll calculations because it automates complex payroll tasks, reducing manual effort and errors.

Standout features & integrations:

Features include built-in tools for complex calculations, multi-user capabilities, and expanded reporting and billing. 

Integrations include NetClient CS, UltraTax CS, Checkpoint Edge, QuickBooks, Xero, ADP, Paychex, Gusto, FreshBooks, and Sage.

Pros and cons


  • Automated payroll tasks
  • Multi-client payroll
  • Efficient batch processing


  • Limited mobile access
  • Higher learning curve

Best for PEO services with 24/7 support

  • From $8/employee/month + $50/month base fee

JustWorks is a comprehensive Professional Employer Organization (PEO) service that provides payroll, benefits, HR, and compliance assistance to businesses. As a payroll software for accountants, it helps streamline various administrative tasks, ensuring businesses remain compliant and efficient.

Why I picked JustWorks:

I chose JustWorks for its comprehensive PEO services combined with around-the-clock support, which is crucial for businesses needing reliable assistance at any time. JustWorks stands out by offering extensive benefits options and compliance support that many other payroll software providers lack. It is best for businesses looking for dedicated PEO services backed by 24/7 support.

Standout features & integrations:

Features include payroll processing, HR tools, compliance management, and access to health insurance plans. It integrates with QuickBooks, Xero, and other accounting software, ensuring seamless data flow and management.

Integrations include QuickBooks, Xero, Gusto, FreshBooks, Wagepoint, Accounting CS Payroll, Patriot Payroll, Paycom, Papaya Global, and Deel.

Pros and cons


  • Easy-to-use platform
  • Comprehensive PEO services
  • 24/7 support


  • Limited customization options
  • Minimum seat requirement
  • Higher starting price

Best for global payroll and compliance management

  • Free demo available
  • Flat rate user pricing, with a free version for businesses with up to 200 people
Visit Website
Rating: 4.8/5

Deel is a global people platform that simplifies payroll, compliance, hiring, onboarding, taxes, invoices, and HRIS for global teams. It stands out due to its ability to handle payroll in 150 countries with full compliance.

Why I picked Deel:

I chose Deel for its comprehensive global payroll and compliance management capabilities. Deel stands out for its ability to manage payroll across 150 countries, ensuring compliance with local laws and regulations. This makes it an ideal choice for companies with a global workforce.

Standout features & integrations:

Features include global payroll, contractor management, equity management, HR operations, performance tools, immigration support, and global compliance. 

Integrations include QuickBooks, Xero, NetSuite, BambooHR, Greenhouse, Workday, Slack, Zapier, Expensify, and Gusto.

Pros and cons


  • Dedicated support
  • Full compliance management
  • Global coverage across 150 countries


  • Better suited to larger organizations
  • Slight learning curve

Best for centralized accounting practice management

  • 30-day free trial
  • From $14.50/user/month
Visit Website
Rating: 4.4/5

Xero is a leading accounting software designed for accountants and bookkeepers, offering streamlined workflows, centralized working, and better collaboration. It stands out for its ability to centralize all accounting tools and client data, making it easier for accountants to manage their practice efficiently.

Why I picked Xero:

I chose Xero for its comprehensive approach to accounting practice management. It is best for centralized accounting practice management because it integrates all tools and client data into a single database, enhancing efficiency and collaboration. Xero's centralized system is ideal for accountants who need to see the big picture quickly and manage multiple clients seamlessly.

Standout features & integrations:

Features include automated admin tasks, tax preparation, and compliance workflows. It also provides a centralized platform for managing clients, staff, and queries. 

Integrations include QuickBooks, FreshBooks, Gusto, Wagepoint, Paycom, Papaya Global, Deel, OnPay, and JustWorks.

Pros and cons


  • Comprehensive client management
  • Automated admin tasks
  • Centralized data management


  • Higher cost than some other tools for advanced features
  • Requires training for new users

Best for AI-driven payments and payroll management

  • Free demo available
  • From $15/employee/month
Visit Website
Rating: 4.5/5

Papaya Global offers a comprehensive platform for global payroll and payments. It excels in managing global workforce payments and ensuring compliance with local regulations.

Why I picked Papaya Global:

Papaya Global stands out for its strength in global payroll and compliance and AI functionalities. This software excels in managing global workforce payments and providing a comprehensive platform for accountants handling international clients.

However, the platform's AI-driven payroll system is what really sets it apart from other payroll tools. Papaya Global leverages AI to ensure accuracy and efficiency, automatically detecting anomalies and potential errors before they become issues. Its seamless integration with various systems, coupled with real-time analytics, provides a user-friendly solution that simplifies complex payroll processes. 

Standout features & integrations:

Features include its Global Workforce Payments, which ensure on-time, regulated, and automated payments, and its Workforce Analytics, providing comprehensive data insights. The platform also offers embedded AI for efficiency and personalized support through Papaya 360 Support and country experts for navigating local payroll and compliance.

Integrations include Workday, NetSuite, SAP, Oracle, QuickBooks, Xero, BambooHR, ADP, Gusto, and Rippling.

Pros and cons


  • Personalized support
  • Automated compliance checks
  • Extensive global coverage


  • Limited customization options
  • Slight learning curve

Other Payroll Software for Accountants

Below is a list of additional payroll software for accountants that I shortlisted, but did not make it to the top list. Definitely worth checking them out.

  1. OnPay

    Best for easy payroll setup and accountant support

  2. QuickBooks Payroll

    Best for seamless integration with QuickBooks

  3. Rippling

    Best for integrating HR and IT management

  4. Namely

    Best for mid-sized companies wanting customizable payroll

  5. SurePayroll

    Best for small businesses seeking easy payroll processing

  6. BrightPay

    Best for UK-based accountants needing bureau features

  7. ADP

    Best for comprehensive payroll and HR solutions

  8. Rise People

    Best for Canadian businesses needing payroll and benefits

  9. Sage for Accountants

    Best for accounting firms needing scalable solutions

If you still haven't found what you're looking for here, check out these tools closely related to accounting software, that we've tested and evaluated.

Payroll Software for Accountants Selection Criteria

When selecting payroll software that truly addresses the needs and pain points of accountants, it's essential to find a tool that goes beyond the basics. I evaluated each option based on its functionality and how well it handles those day-to-day tasks. Here are the criteria I used to determine how these tools should perform to meet your specific payroll management needs:

Core Functionality - 25% of total weighting score

  • Accurate payroll processing
  • Tax calculation and filing
  • Direct deposit capabilities
  • Employee self-service portals
  • Compliance management

Additional Standout Features - 25% of total weighting score

  • Integration with accounting software
  • Customizable reporting tools
  • Mobile access for on-the-go management
  • Advanced security features
  • AI-driven insights and analytics

Usability - 10% of total weighting score

  • Intuitive user interface
  • Drag-and-drop functionality
  • Customizable dashboards
  • Easy navigation and accessibility
  • Minimal learning curve

Onboarding - 10% of total weighting score

  • Availability of training videos
  • Interactive product tours
  • Chatbots for instant support
  • Webinars for in-depth learning
  • Pre-built templates for quick setup

Customer Support - 10% of total weighting score

  • 24/7 customer service availability
  • Multiple support channels (phone, email, chat)
  • Dedicated account managers
  • Comprehensive help center
  • Fast response times

Value For Money - 10% of total weighting score

  • Competitive pricing plans
  • Transparent pricing structure
  • Free trial or demo availability
  • Cost-benefit analysis
  • Discounts for long-term commitments

Customer Reviews - 10% of total weighting score

  • Overall satisfaction ratings
  • Feedback on ease of use
  • Comments on customer support quality
  • Reviews on feature effectiveness
  • Testimonials on reliability and performance

These criteria ensure that the payroll software selected meets the specific needs of accountants, addressing their pain points and providing the necessary functionality for efficient payroll management.

Payroll software is evolving rapidly. Here are some key trends to watch.

  • AI-Powered Automation: AI is automating repetitive payroll tasks. This reduces errors and saves time. It's crucial for efficiency.
  • Cloud-Based Solutions: Cloud-based payroll software is gaining traction. It offers accessibility from anywhere. This is vital for remote work.
  • Integration with HR Systems: Payroll software is integrating with HR systems. This unifies employee data. It simplifies management.
  • Enhanced Data Security: Data security features are improving. Protecting sensitive payroll information is a priority.
  • Mobile Accessibility: Mobile-friendly payroll software is on the rise. It allows on-the-go access. This is important for flexibility.

Expect to see AI doing more of the heavy lifting, intuitive integrations with HR systems for better employee self-serve options, and continuous security improvements to keep your data safe. These trends are shaping the future of accounting software, so keep an eye out as you navigate your options for the best fit for your business.

What Is Payroll Software for Accountants?

Payroll software for accountants is a tool designed to automate and manage the process of paying employees. Accountants and HR professionals use it to calculate wages, withhold taxes, and ensure compliance with labor laws.

The software typically includes components such as payroll calculation, tax filing, direct deposit, and reporting. It helps users manage employee data, track hours worked, and generate pay stubs, ensuring accurate and timely payroll processing.

Features of Payroll Software for Accountants

When choosing payroll software, there are the non-negotiables and the nice-to-haves. As an accountant shopping for payroll software, here are the most important features you’ll want to consider:

  • Automated Tax Calculations: Ensures compliance with tax regulations by automatically calculating federal, state, and local taxes.
  • Direct Deposit: Allows employees to receive their pay directly into their bank accounts, reducing the need for paper checks.
  • Employee Self-Service Portal: Empowers employees to access their pay stubs, tax forms, and personal information, reducing administrative workload.
  • Time and Attendance Tracking: Integrates with time-tracking systems to ensure accurate payroll processing based on actual hours worked.
  • Compliance Management: Keeps the software updated with the latest labor laws and tax codes which CPAs can appreciate as this helps to maintain adherence to local, state, and federal regulations effortlessly.
  • Customizable and Advanced Reporting: Provides detailed payroll reports that can be customized to meet specific business needs and aid in financial analysis. 
  • Integration with Accounting Software: Seamlessly connects with accounting systems to ensure accurate financial records and simplify bookkeeping.
  • Benefits Management: Manages employee benefits such as health insurance, retirement plans, and other perks, ensuring accurate deductions and contributions.
  • Multi-State and International Payroll: Supports payroll processing for employees in different states or countries, ensuring compliance with various regulations.
  • Security Features: Protects sensitive payroll data with encryption, user access controls, and regular security updates.

Choosing payroll software with these features will help not only streamline payroll processes, but ensure compliance and reduce administrative burdens.

Benefits of Payroll Software for Accountants

Payroll software has become an essential tool for accountants, offering numerous advantages that streamline payroll processes and enhance overall efficiency. For organizations and accountants considering the adoption of payroll software, understanding its benefits can help in making an informed decision. Below are five main benefits of payroll software for accountants:

  • Time-Savings: Payroll software automates many of the repetitive and time-consuming tasks involved in payroll processing, such as calculating wages, taxes, and deductions. This allows you to focus on more strategic tasks and reduces the time spent on manual data entry which also means cost-savings.
  • Improved Accuracy: By automating calculations and data entry, payroll software significantly reduces the risk of human error. This ensures that employees are paid accurately and on time, and helps avoid costly mistakes related to tax filings and compliance.
  • Compliance Management: Payroll software helps ensure compliance with ever-changing tax laws and employment regulations. It automatically updates tax rates and generates necessary reports, reducing the risk of non-compliance and associated penalties.
  • Enhanced Data Security: Payroll software provides robust security features, such as data encryption and secure access controls, to protect sensitive employee information. This helps prevent data breaches and ensures that confidential information is handled securely.
  • Employee Self-Service: Many payroll software solutions offer self-service portals that allow employees to access their pay stubs, tax forms, and other payroll-related information online. This reduces the administrative burden on HR and payroll staff and empowers employees to manage their own payroll information.

Payroll software offers significant benefits for accountants and organizations, including time savings, improved accuracy, compliance management, enhanced data security, and employee self-service. By adopting payroll software, accountants can streamline their payroll processes, reduce errors, and focus on more strategic tasks, ultimately contributing to the overall efficiency and success of the organization.

Costs & Pricing of Payroll Software for Accountants

When considering payroll software for accountants, it's essential to understand the various pricing models and features available. Payroll software can significantly streamline payroll processes, reduce errors, and ensure compliance with tax regulations. However, the costs can vary widely depending on the features and services included in each plan. 

Below, we provide a detailed overview of different payroll software plans, their average prices, and common features to help you make an informed decision.

Plan Comparison Table for Payroll Software for Accountants

Plan TypeAverage PriceCommon Features
Free Plan$0Basic payroll processing, direct deposit, employee self-service, and limited support
Basic Plan$10/month + $4/employeePayroll processing, direct deposit, printable W-2s, setup, and expert support
Standard Plan$40/month + $6/employeeFull-service payroll, employee self-service, tax filing, direct deposit, and reports
Premium Plan$80/month + $12/employeeAdvanced payroll features, next-day direct deposit, HR support, and compliance alerts
Enterprise Plan$125/month + $10/employeeFull-service payroll, tax penalty protection, dedicated support, and advanced reporting
A breakdown of plan types, costs, and features for payroll software for accountants.

When choosing software to run payroll, consider the size of your business, the complexity of your payroll needs, and the level of support required. Each plan offers different features and pricing, so it's essential to select one that aligns with your specific requirements and budget.

Payroll Software for Accountants FAQs

Here are some answers to frequently asked questions you may have about payroll software and how it works:

How does payroll software integrate with accounting software?

Integration between payroll and accounting software is crucial for seamless financial management. Most payroll software offers direct integration with popular accounting platforms like QuickBooks, Xero, and FreshBooks. This integration ensures that payroll data is automatically synced with the accounting software, reducing the need for manual data entry and minimizing errors. For example, QuickBooks Online Payroll integrates directly with QuickBooks Online Accounting, updating the general ledger with payroll-related expenses automatically.

Can payroll software handle multi-state payroll?

Yes, many payroll software solutions can handle multi-state payroll, which is essential for businesses with employees in different states. For example, OnPay allows you to set up tax rates for multiple states at no additional cost, and Gusto supports multi-state payroll capabilities. This feature ensures compliance with varying state tax laws and regulations.

Is it legal to pay employees in cash?

Yes, it is legal to pay employees in cash, but it requires meticulous record-keeping to ensure compliance with tax laws. Employers must withhold taxes and provide accurate pay stubs, just as they would with other payment methods. Paying in cash can attract scrutiny from tax authorities, so it is generally recommended to use more traceable payment methods like direct deposit.

What is the difference between exempt and nonexempt employees?

Exempt employees are not entitled to overtime pay under the Fair Labor Standards Act (FLSA) and must meet specific criteria, such as earning a salary of at least $35,568 per year and performing executive, administrative, or professional duties. Nonexempt employees, on the other hand, are entitled to overtime pay for hours worked over 40 in a workweek. The distinction is crucial for compliance with labor laws and proper payroll processing.

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Simon Litt
By Simon Litt

Simon Litt is the editor of The CFO Club, specializing in covering a range of financial topics. His career has seen him focus on both personal and corporate finance for digital publications, public companies, and digital media brands across the globe.