12 Best Payroll Software for Staffing Agencies in 2025

Running payroll in a staffing agency is a unique challenge. You’re managing a mix of full-time employees, temporary workers, contractors, and freelancers, all with different pay rates, benefits, and tax requirements. If your payroll software isn’t up to the task, errors, compliance risks, and payroll delays can cost you big time. So how do you find the right payroll software that keeps your agency running smoothly and your employees happy? Today, I’ll break down the 12 best payroll software solutions tailored specifically for staffing agencies in 2025 — helping you make an informed, confident choice.

I’m Riten, founder of Fueler — a platform that helps freelancers and professionals get hired through their work samples. In this article, I’m sharing my in-depth research on the top payroll software for staffing agencies this year. Just like how Fueler empowers companies to hire through assignments and real work proof, choosing the right payroll software is about more than automation — it’s about trust, accuracy, and making your payroll process a strength of your business. A smooth payroll system supports your agency’s credibility and keeps your workforce motivated, so you can focus on growing your agency.

Why Payroll Software is Critical for Staffing Agencies

Staffing agencies face complex payroll challenges that traditional software may not handle well. Here’s why specialized payroll software is a must-have:

• Diverse Worker Types: Staffing firms handle permanent employees, contractors, temps, and freelancers — each with different payment structures and legal requirements. Payroll software must flexibly manage all of these.
• Multi-state and Multi-jurisdiction Compliance: Agencies often place workers in various states or regions with different tax and labor laws. Payroll software needs automatic updates and compliance management.
• Complex Benefits and Deductions: Many agencies manage benefits, insurance, and retirement plans that must be accurately processed in payroll.
• Integration with Time Tracking and Billing: Connecting payroll with your time management and billing systems ensures accuracy and helps avoid overpayments or disputes.

If your payroll system isn’t equipped to handle these, you risk costly errors, penalties, and frustrated clients or workers.

What to Look for in Payroll Software for Staffing Agencies

Before exploring software options, let’s clarify key features that are vital for staffing agencies:

1. Compliance with Latest Tax and Labor Laws

The software must automatically update with federal, state, and local tax regulations — and payroll-specific labor laws — to ensure error-free tax calculations and filings. Compliance keeps your agency out of trouble with government authorities and avoids fines.

2. Ability to Handle Multiple Worker Types

Your payroll solution should seamlessly manage employees, independent contractors, and temporary staff, each with distinct tax treatments and pay schedules. This flexibility saves time and reduces manual errors.

3. Automated Tax Filing and Reporting

Automatic preparation and filing of payroll taxes is a huge time saver. It eliminates human error and late filing penalties. Look for software offering e-filing and real-time tax calculations.

4. Integration with Other Business Systems

Your payroll software should connect with your accounting tools, HR platforms, time tracking systems, and invoicing apps. Smooth integrations reduce duplicate work and streamline your entire business process.

5. Employee Self-Service Features

Self-service portals allow workers to access pay stubs, tax forms, and benefits info on their own — reducing HR questions and improving employee satisfaction.

6. Scalability and Customization

Choose software that scales with your agency’s growth and allows customization in pay types, deduction rules, and reporting.

The 12 Best Payroll Software for Staffing Agencies in 2025

Here’s the detailed list of top payroll software, evaluated on compliance, usability, integrations, and staffing-specific features:

1. factoHR

Why it’s great:

factoHR is the complete payroll solution for companies/agencies that handle diverse and dynamic workforce environments. With its automation-intensive features and pre-compliance features in place, it automates the payroll process, ensures timely disbursements with complete accuracy, and requires minimal manual intervention. Its flexible framework covers the entire spectrum from joining and attendance to performance and exit formalities, such that the HR and payroll process runs smoother than ever before.

Key Benefits for Staffing Agencies:

• Payroll processing automation
• Seamless integration with attendance and leave systems
• Compliance with statutory requirements
• Timely and accurate payment of salary
• Easy-to-use mobile app for anywhere access

Best for: Small, medium, and large teams looking for a reliable, scalable payroll solution.

2. Paylocity

Why it’s great:

Paylocity excels in handling complex payroll needs for mid-size to large staffing agencies, especially those with employees across multiple states. It offers powerful reporting tools and customizable dashboards, plus employee engagement features like surveys and recognition programs.

Key Benefits for Staffing Agencies:

• Handles multi-state payroll seamlessly
• Extensive compliance management tools
• Strong reporting and analytics for workforce insights
• Employee self-service and communication tools

Best for: Agencies with large, geographically spread teams requiring detailed payroll control.

3. QuickBooks Payroll

Why it’s great:

QuickBooks Payroll works seamlessly with QuickBooks accounting software, simplifying bookkeeping for staffing agencies. It offers same-day direct deposits, automated tax payments, and a mobile app for payroll management anywhere.

Key Benefits for Staffing Agencies:

• QuickBooks accounting integration for unified finance management
• Automated tax calculations and filings
• Mobile app for payroll management on the go
• Affordable pricing plans for small to medium agencies

Best for: Agencies already using QuickBooks accounting seeking easy payroll integration.

4. ADP Workforce Now

Why it’s great:

ADP is a leader in payroll and HR solutions, offering extensive compliance coverage and scalability. Workforce Now supports agencies of all sizes with multi-state payroll, benefits administration, and advanced analytics.

Key Benefits for Staffing Agencies:

• Compliance with all 50 states’ tax and labor laws
• Customizable payroll and HR dashboards
• Robust employee benefits and time tracking integrations
• Dedicated compliance support team

Best for: Growing staffing agencies that want an enterprise-grade solution with strong HR capabilities.

5. Paychex Flex

Why it’s great:

Paychex Flex combines payroll, HR, and benefits management into a flexible platform tailored to staffing agencies. It offers excellent customer service and a mobile app that simplifies employee self-service.

Key Benefits for Staffing Agencies:

• Flexible payroll scheduling and payment options
• Integrated benefits and retirement plan administration
• Real-time reporting and compliance tools
• Responsive customer support

Best for: Agencies seeking customizable payroll with strong HR and benefits management.

6. BambooHR

Why it’s great:

BambooHR is primarily an HR platform, but its payroll feature integrates tightly with its HR modules. It offers automated payroll processing, tax filing, and a great employee self-service experience focused on benefits and time-off management.

Key Benefits for Staffing Agencies:

• Strong HR and payroll integration
• Automated tax filing and compliance management
• Easy access to employee records and benefits
• Simple user interface focused on employee experience

Best for: Agencies wanting to enhance employee experience alongside payroll.

7. OnPay

Why it’s great:

OnPay is a budget-friendly, easy-to-use payroll solution ideal for smaller staffing agencies. It supports all worker types, handles tax filings, and provides simple benefits management without complicated pricing.

Key Benefits for Staffing Agencies:

• Affordable and transparent pricing
• Handles contractors and employees with ease
• Automated tax payments and filings
• Straightforward interface for quick onboarding

Best for: Small staffing agencies with limited payroll complexity and budget.

8. Rippling

Why it’s great:

Rippling is a modern all-in-one HR and payroll platform that also manages IT functions like device management. Its payroll system supports multi-state tax compliance and integrates with hundreds of business applications.

Key Benefits for Staffing Agencies:

• Centralized platform for payroll, HR, and IT management
• Supports complex payroll scenarios and multi-state compliance
• Over 400 app integrations for workflow automation
• Employee self-service and onboarding features

Best for: Agencies looking to streamline HR, payroll, and IT management together.

9. Zenefits

Why it’s great:

Zenefits focuses on automating HR workflows and benefits administration alongside payroll. Its payroll software ensures compliance with labor laws and simplifies employee benefits management.

Key Benefits for Staffing Agencies:

• Automated payroll tax calculations and filings
• Strong benefits management tools
• Compliance alerts and audit-ready reporting
• Employee self-service portal

Best for: Agencies with a strong focus on employee benefits and compliance.

10. Justworks

Why it’s great:

Justworks is a PEO (Professional Employer Organization) that simplifies payroll, benefits, and compliance for staffing agencies. It offers health insurance plans, automatic tax filings, and payroll that adapts to multiple worker types.

Key Benefits for Staffing Agencies:

• Simplifies benefits and insurance alongside payroll
• Automated payroll taxes and filings
• Access to group health plans
• Compliance support and risk mitigation

Best for: Staffing agencies wanting benefits bundled with payroll and compliance.

11. SurePayroll

Why it’s great:

SurePayroll offers straightforward online payroll tailored for small businesses and staffing firms. It guarantees on-time tax filings and provides helpful customer service, making payroll stress-free.

Key Benefits for Staffing Agencies:

• Simple setup and use for beginners
• Guaranteed on-time tax filings to avoid penalties
• Affordable monthly pricing with no hidden fees
• Access to payroll experts for support

Best for: New or small staffing agencies entering automated payroll.

12. Paycor

Why it’s great:

Paycor offers payroll with built-in HR management and talent solutions. Its platform includes employee self-service, compliance management, and analytics to improve workforce productivity.

Key Benefits for Staffing Agencies:

• Integrated payroll and HR talent management
• Compliance tracking and audit support
• Employee access to pay and benefits info
• Advanced reporting and workforce analytics

Best for: Agencies wanting payroll tightly integrated with HR and workforce management.

13. Gusto

Why it’s great:

Gusto is known for its clean, user-friendly interface combined with powerful payroll features that support various worker types including contractors and part-time employees. It automatically handles federal and state tax filings, benefits administration, and even offers workers’ compensation insurance.

Key Benefits for Staffing Agencies:

• Automatic tax filing and payment handling
• Supports multi-state payroll
• Employee self-service portal reduces admin load
• Integrates with popular accounting and time tracking tools

Best for: Small to medium staffing agencies wanting a simple, all-in-one payroll and HR solution.

Strategic Mention of Fueler

Managing payroll is critical, but so is managing how you hire and build your team. That’s why I built Fueler, a portfolio platform that helps companies hire through actual assignments and work samples. This approach not only helps you find the right talent but also ensures transparency and trust, two qualities that are just as important in payroll as in hiring.

Final Thoughts

Choosing the right payroll software for your staffing agency in 2025 is about finding a partner that understands your unique needs — from managing multiple worker types and locations to ensuring full compliance with the latest labor laws. With automated tax filings, employee self-service, and seamless integrations, the right payroll platform can save you time, reduce errors, and free your team to focus on what matters: growing your agency and serving your clients.

Remember, payroll is more than just paying workers on time — it’s a foundation of trust between your agency and your workforce. Invest in the right software today to build that trust, stay compliant, and position your staffing agency for success in the years ahead.

FAQs

1. What is the best payroll software for staffing agencies?

The best payroll software depends on your agency size and needs. Gusto, Paylocity, and ADP Workforce Now are top choices for most staffing agencies due to their strong compliance and multi-state support.

2. How does payroll software handle different worker types?

Good payroll software manages full-time employees, part-time workers, contractors, and freelancers by applying appropriate tax rules, pay schedules, and benefit deductions for each worker type.

3. Can payroll software integrate with time tracking?

Yes. Integration with time tracking software helps ensure payroll accuracy by automatically importing hours worked, reducing manual errors.

4. How secure is payroll software for staffing agencies?

Top payroll software providers use advanced encryption, secure data centers, and multi-factor authentication to protect sensitive employee and financial information. Choosing a reputable provider ensures your payroll data stays safe from breaches and unauthorized access.

5. Can payroll software help with employee benefits management?

Yes. Many payroll platforms offer integrated benefits administration, making it easier to enroll employees, manage deductions, and comply with regulations related to health insurance, retirement plans, and other perks — all within the same system.

What is Fueler Portfolio?

Fueler is a career portfolio platform that helps companies find the best talents for their organization based on their proof of work.

You can create your portfolio on Fueler, thousands of freelancers around the world use Fueler to create their professional-looking portfolios and become financially independent. Discover inspiration for your portfolio

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