Staffing agencies manage payroll in a uniquely demanding environment handling multiple pay rates, rapid onboarding, frequent job changes, and compliance requirements across different clients and states. A reliable payroll system must support both W-2 employees and 1099 contractors, integrate with recruiting tools, and accurately process high-volume weekly or biweekly payroll cycles. The right platform reduces administrative overhead, minimizes errors, and helps agencies maintain profitability through accurate job costing and billing. This guide compares the best payroll solutions for staffing agencies of all sizes, highlighting the tools that simplify complex workflows and keep agencies compliant as they grow.
Gusto
Best all-in-one payroll & HR platform for staffing agencies
Gusto is the best all-in-one payroll and HR platform for staffing agencies that need to manage both W-2 employees and 1099 contractors, streamline onboarding, and handle multiple pay rates. With seamless payroll, benefits, and HR tools in one system, Gusto gives staffing firms a simple, unified workflow that reduces administrative overhead and improves accuracy. Its integrations and automated tax filing also help staffing firms stay compliant as they scale.
Key Features
Full-service payroll with automated federal, state, and local tax filing
Support for W-2 employees and 1099 contractors
Automated onboarding with digital forms and e-signatures
Multi-rate pay structures and assignment tracking
Time tracking and PTO management
Benefits administration and contractor benefits options
Employee self-service portal for pay, forms, and bookings
Integrations with applicant tracking systems (ATS) and accounting tools
Contractor payment options and tax-reporting tools
Compliance alerts and audit-ready documentation
Pros and Cons
Pros
All-in-one HR + payroll– reduces complexity for staffing firms
Easy to set up and use—ideal for small to mid-sized agencies
Transparent pricing and no hidden fees
Strong integrations with ATS and accounting systems
Includes contractor and W-2 support in one system
Cons
May not have some of the advanced workforce analytics found in niche staffing HRIS
Benefits administration is less extensive for contractors than some specialist platforms
Might require add-on integrations for very high-volume staffing operations
Pricing
Simple: $49/month + $6/person/month
Plus: $80/month + $12/person/month
Free trial: Yes — free until first payroll
Free plan: No
Patriot Payroll
Best low-cost payroll solution for small staffing agencies
Patriot Payroll is an affordable payroll platform ideal for small staffing agencies or new firms that need to run payroll for both employees and contractors without paying for extra HR features. With simple workflows, multiple pay-rate options, and clear pricing, Patriot offers a cost-effective way for staffing firms to manage weekly or biweekly payroll while staying compliant. It's especially useful for agencies with tight budgets or fluctuating headcounts.
Key Features
Full-service or basic payroll options
Support for W-2 employees and 1099 contractors
Multiple pay rates and pay frequency options
Time and attendance add-on
Direct deposit or printable checks
Employee self-service portal
Automated W-2 and 1099 filing (in Full-Service plan)
Integrations with popular accounting tools
Customizable deductions and contributions
Payroll reports for billing and auditing
Pros and Cons
Pros
Very affordable pricing compared to most providers
Handles W-2 and contractor payments
Easy to use and simple to set up
Flexible pay-rate configuration for staffing assignments
Cons
Limited HR features without add-ons
Fewer integrations than full HRIS platforms
Basic plan does not include tax filing
Not ideal for larger agencies with complex compliance needs
Pricing
Basic Payroll: Low monthly base fee + per-employee fee (no tax filing)
Full-Service Payroll: Higher base fee + per-employee fee (tax filing included)
Optional add-ons for Time & Attendance and HR
Month-to-month billing with no long-term contracts
OnPay
Best for staffing agencies needing simple, flexible payroll & contractor support
OnPay is an excellent option for staffing agencies that need an intuitive, flexible payroll system capable of handling W-2 employees, seasonal workers, and 1099 contractors. With automated tax filing, unlimited pay runs, and strong support for variable pay rates, OnPay streamlines payroll for agencies that move workers between assignments. Its nonprofit and small business focus also makes it a great choice for agencies that want clarity, accuracy, and straightforward monthly pricing.
Key Features
Full-service payroll with automated tax filing
Unlimited monthly pay runs
Supports W-2 employees and 1099 contractors
Multiple pay rates and job assignments
Time tracking and PTO management
Automated onboarding with e-signatures
Benefits administration (health, dental, vision, retirement)
Customizable payroll reports for billing and job costing
Integrations with QuickBooks, Xero, and HR tools
Employee self-service for pay stubs and tax forms
Pros and Cons
Pros
Transparent, all-inclusive pricing
Excellent support for pay-rate changes and contractor payments
Clean interface that’s easy for office staff to learn
Unlimited pay runs—ideal for weekly staffing payroll cycles
Cons
Lacks advanced workforce analytics
Not designed for very large or enterprise staffing firms
Fewer native integrations than larger HRIS platforms
Benefits availability varies by state
Pricing
$40/mo + $6 per person
Includes full-service payroll, tax filings, onboarding, and contractor payments.
Time tracking and benefits available as add-ons
EPAY Systems
Best for staffing agencies with complex scheduling & labor compliance needs
EPAY Systems is a robust HCM and payroll platform designed for staffing agencies that manage large hourly workforces, multiple job placements, and strict labor compliance requirements. With advanced time tracking, workforce analytics, and pay-rule automation, EPAY is ideal for agencies that place workers across different client sites or industries. Its unified suite helps agencies reduce payroll errors, maintain compliance, and streamline the entire employee lifecycle.
Key Features
Full-service payroll with automated multi-state tax filing
Advanced time and attendance with mobile, biometric, and GPS options
Shift, job, and location-based pay rules
Labor compliance tools and audit-ready reporting
Scheduling and workforce management modules
Onboarding and document management
HR suite with performance and learning tools
Integrations with ATS and accounting systems
Analytics dashboards for labor, costs, and client billing
Pros and Cons
Pros
Built for complex, high-volume staffing operations
Excellent compliance tools for multi-state and multi-client placements
Powerful time tracking and pay-rule automation
Scales well for agencies with hundreds or thousands of workers
Cons
More expensive than small-business payroll platforms
Requires training and implementation
Too robust for small staffing agencies
Custom pricing is needed for most modules
Pricing
Quote-based pricing depending on modules and workforce size
Payroll, time tracking, HR, and scheduling sold in bundles
Implementation and onboarding packages required
Enterprise contracts common for staffing clients
Paylocity
Best for mid-sized staffing agencies needing scalable payroll & HR tools
Paylocity is a scalable payroll and HR platform well-suited for mid-sized staffing agencies that need more than basic payroll. With strong automation, advanced reporting, and integrated HR tools, Paylocity helps agencies manage workers across multiple clients, states, and job assignments. Its modern interface, powerful compliance features, and self-service capabilities make it a strong choice for agencies that need both flexibility and depth.
Key Features
Full-service payroll with automated multi-state tax filing
Support for W-2 and 1099 worker types
Advanced reporting and analytics for labor, billing, and job costing
Time and attendance with geofencing and mobile clock-ins
Onboarding, applicant tracking, and document management
Benefits administration and ACA compliance
Learning management and performance tools
Mobile self-service for employees, recruiters, and managers
Integrations with ATS, VMS, and accounting tools
Pros and Cons
Pros
Scalable for growing staffing agencies
Strong reporting and compliance capabilities
Integrates well with ATS and workforce tools
Modern UX that’s easy for staff to adopt
Cons
Pricing is higher than small-business platforms
Implementation can take time
Some features require additional add-ons
Not designed exclusively for staffing agencies
Pricing
Quote-based pricing depending on module selection and headcount
Payroll, HR, time tracking, and benefits available in modular add-ons
Implementation and support included for most plans
Annual contract required
Rippling
Best for staffing agencies managing mixed W-2 and 1099 workforces
Rippling is an ideal platform for staffing agencies that need to manage both W-2 employees and 1099 contractors across multiple clients, job sites, and states. Its unified payroll, HR, IT, and time-tracking ecosystem allows agencies to automate onboarding, run multi-rate payroll, and integrate with their ATS without manual data entry. Rippling's flexibility and modular design make it especially powerful for agencies that frequently transition workers between assignments or manage multiple pay structures.
Key Features
Full-service payroll with automated federal, state, and local tax filing
Handles W-2 and 1099 workers with ease
Multi-rate and location-based pay rules
Automated onboarding that syncs with ATS systems
Time tracking, scheduling, and labor management
Benefits administration and compliance monitoring
Global payroll options for staffing firms placing remote workers
Unified HR + IT system for provisioning equipment and access
Analytics and custom reporting for job costing and billing
Pros and Cons
Pros
Extremely flexible for multi-client staffing workflows
Powerful automation across payroll, HR, and IT
Excellent integrations with ATS, CRM, and accounting tools
Scales well from small agencies to enterprise staffing firms
Cons
More expensive than basic payroll tools
Modular pricing can add up quickly
Implementation may require additional setup
Some advanced features are only available in higher tiers
Pricing
Modular pricing starting with a per-employee platform fee
Payroll, HR, IT management, and time tracking sold as add-ons
Custom quotes for larger staffing firms or global payroll
Annual agreements common for full-suite deployments
Avionté
Best end-to-end staffing platform with integrated payroll
Avionté is a full end-to-end staffing platform designed specifically for staffing and recruiting agencies.It combines applicant tracking, onboarding, timekeeping, billing, and payroll into a single system eliminating the need for multiple point solutions. For agencies that want a unified workflow from talent acquisition through payroll and invoicing, Avionté provides one of the most complete ecosystems available. It's especially strong for light industrial, clerical, and healthcare staffing firms that need high-volume processing and compliance support.
Key Features
Fully integrated payroll with automated tax filing
Applicant tracking and recruiting CRM
Onboarding and digital document management
Timekeeping with mobile, kiosk, and biometric options
Multi-rate, multi-assignment payroll processing
Client billing and invoicing tools
Job costing, margin tracking, and profitability reporting
Compliance tools for E-Verify, ACA, and safety
Vendor management and customer portals
Mobile apps for recruiters and talent
Pros and Cons
Pros
Built specifically for staffing agencies
End-to-end platform reduces manual data transfers
Excellent for high-volume hourly placements
Strong reporting for profitability and client billing
Cons
More complex than small agencies may need
Higher cost than standalone payroll tools
Requires formal implementation
Interface can feel dense for new users
Pricing
Custom, tiered pricing based on agency size
Payroll, ATS, CRM, timekeeping, and billing offered as unified suite
Implementation and training packages required
Annual contracts standard for staffing industry deployments
WorkforceHub
Best payroll + scheduling + time tracking solution for small staffing agencies
WorkforceHub is a streamlined HR, scheduling, and time-tracking platform designed for small staffing agencies that need simple, reliable workforce management alongside payroll. It supports multi-location timekeeping, shift assignments, and accurate pay calculations making it ideal for agencies placing hourly workers in retail, hospitality, light industrial, home care, and other shift-based roles. WorkforceHub offers an intuitive, lightweight alternative to full-suite systems while still delivering the core tools staffing firms rely on.
Key Features
Full-service payroll with automated tax filing
Time tracking with mobile, kiosk, and geofencing options
Scheduling and shift assignment tools
PTO tracking and accrual automation
Employee self-service portal
Onboarding and document management
Built-in compliance tools (breaks, overtime, state rules)
Integrations with accounting and HR systems
Custom payroll reports for client billing and job costing
Pros and Cons
Pros
Simple, intuitive platform for small staffing firms
Built-in scheduling + time tracking for hourly placements
Flexible enough for multiple job sites or clients
More affordable than large enterprise HR suites
Cons
Not designed for high-volume or enterprise staffing agencies
Basic ATS features compared to specialized recruiting tools
Limited analytics compared to larger platforms
Some features require additional modules
Pricing
Quote-based pricing depending on headcount and modules
Payroll and time tracking offered as core features
Optional add-ons for HR tools and scheduling
Month-to-month or annual agreements available
FAQ
How do staffing agencies pay employees?
Staffing agencies typically run weekly or biweekly payroll for W-2 employees placed at client worksites. Agencies bill clients for hours worked, then use payroll software to calculate wages, overtime, taxes, and deductions. Many agencies also pay 1099 contractors, making it essential to use a payroll system that supports both worker types and multiple pay rates.
Is it better to outsource payroll or do it myself?
For staffing agencies, outsourcing payroll or using a full-service payroll platform is usually the better option. Agencies deal with complex pay rules, frequent job changes, and multi-state compliance requirements. Outsourcing reduces administrative burden and helps prevent costly payroll and tax errors, especially when handling high-volume hourly workforces.
What is the cheapest way to pay employees?
The lowest-cost method is to use manual payroll or basic calculators, but this is risky for staffing agencies due to multi-rate pay structures and compliance requirements. Among paid tools, low-cost providers like Patriot and OnPay offer some of the most affordable full-service payroll plans while still supporting contractors and hourly employees.
How much percentage do staffing agencies take?
Most staffing agencies charge clients a markup of 20% to 75% on the worker's hourly wage, depending on industry, role complexity, and market demand. This markup covers payroll taxes, workers' compensation, administrative costs, and profit margin. Specialized placements may command higher markups.
What is staffing payroll?
Staffing payroll refers to the process of paying workers placed at client companies, including W-2 employees and sometimes 1099 contractors. It involves calculating hourly wages, overtime, job-specific pay rates, taxes, and deductions often across multiple job sites or states. Because staffing agencies manage complex, high-volume pay cycles, payroll systems must support multi-rate assignments, rapid onboarding, and accurate job costing.