Enterprise payroll services, 50–1,000+ employees

An enterprise payroll solution built for the needs of midsize and large companies

Even simple payroll processes can expose a company to potential wage and hour and tax penalties. And the more complex your business, the greater effect inaccurate data and tax issues may have on your company’s bottom line.

Help reduce risk by managing your company’s enterprise payroll software with Paychex Flex®, our human capital management (HCM) software. Scalable to support businesses with as few as 50 employees to those with thousands, and configurable to meet your organization’s needs, Paychex Flex can help your company streamline enterprise payroll and stay up to date with the latest tax rates.

  • End-to-end HCM

    Save time and help reduce data-entry errors with a comprehensive HCM solution integrating payroll and taxes, recruiting, onboarding, and more. 

  • Employee self-service

    Give employees the ability to view their check stubs, W-2s, and more from their desktop or mobile device.

  • Flexible, U.S. based service

    Work with a specialist in large business payroll and get answers when you need them through our 24/7 service centers.

  • Import multiple files

    With our intuitive multi-import user interface, single company and multi-company users can import multiple files for a single company and/or multi companies at one time, from one location.

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Paychex Flex makes enterprise payroll effortless

  • Enter payroll quickly and easily

    Easily enter and submit your data with our enterprise payroll software. Set up recurring amounts to save even more time each pay period.

  • View critical data at a glance

    Key info, such as upcoming check dates and cash required for your next payroll, is available right from the main dashboard.

  • Run reports

    Access payroll reports with multi-level tracking by location, department, job, project, and union tracking by date range.

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What you can get with Paychex enterprise payroll

  • Online payroll processing
  • Direct deposit, paper checks, and paycards
  • Ability to pay different types of workers — salaried, hourly, contract
  • Automatic payroll tax administration
  • Employee online self-service
  • New-hire reporting to government agencies
  • Free mobile app for you and your employees
  • Labor poster kit
  • Garnishment payments
  • Robust reporting and analytics

A more effective enterprise payroll solution

  • Integrated system for payroll, HR, and more

    Paychex Flex isn’t just for enterprise payroll; it’s a complete HCM solution:

    • Recruiting
    • Hiring and onboarding
    • Time and attendance
    • Payroll
    • HRMS
    • Benefits
    • Retirement

    Accessing these services from one platform can help your organization share data and analytics across departments, collaborate more effectively, and reduce the risk of errors and penalties.

  • Robust analytics and reporting
    • Analyze payroll labor costs across time and departments.
    • Quickly view your payroll journal, employee earnings record, check stub, cash requirements, department summary, tax deposit, and year-to-date reports from the dashboard.
    • Access 160+ payroll and HR reports and customize them to your needs.
    • Discover if labor supply met demand with labor costs trends analytics that compares pay periods side by side.

    Learn more about Paychex Flex workforce analytics.

  • Multiple employee pay options
    • Direct deposit
    • Same-day ACH capability to pay employees in time-sensitive scenarios.*
    • Paper checks with check signing and insertion services
    • Paycards for employees who may not have a bank account but may still benefit from direct deposit.
  • Import to your accounting software with general ledger service

    Keying in payroll information to your accounting software by hand can be tedious and error-prone. Using a secure online process, Paychex lets you easily post payroll data to your accounting program from our enterprise payroll software. Compatible software includes:

    • QuickBooks®
    • Sage Intacct
    • Xero™
  • Job costing and labor distribution

    Our system includes a payroll journal and the data you need for job costing and labor analysis. View a list of departmental costs, including earnings, employer taxes, and employer expenses.

  • Wage garnishment payments

    Help protect your company by processing garnishments within federal and state laws. Paychex Flex can help calculate garnishment wages, make deductions from your employees’ wages, and pay the appropriate agency.

Something else to consider

Time and Attendance

Gain back lost time spent on entering or importing time cards, and help ensure you’re paying employees for time actually worked, with an online time and attendance system integrated with payroll.
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