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Paychex vs CheckMark Payroll: Which Payroll Software Is Better?


Disclosure: We may earn commissions if you shop through the links below.

Last Updated: May 22, 2025

Both Paychex and CheckMark Payroll are leading payroll software solutions, but which one is better for you and your business?

Below we compare Paychex and CheckMark Payroll across nearly 50 different data points to help you make find the right one.

 

Paychex vs CheckMark Payroll Reviews

PaychexCheckMark Payroll
Trustpilot Rating1.23.5
Number of Trustpilot Reviews2330
iPhone App Rating4.8not available
Number of iPhone App Reviews411200not available
Android App Rating3.8not available
Number of Android App Reviews29400not available

Paychex vs CheckMark Payroll Pricing

PaychexCheckMark Payroll
Free Trialn/aYes
Free Trial Lengthn/a2 months
Cheapest Plan NameEssentialsCheckMark Payroll Pro
Cheapest Plan Cost Per Month$By request$n/a
Mid Priced Plan NameSelectn/a
Mid Priced Plan Cost Per Month$By request$n/a
Top Plan NameProCheckMark Payroll Pro+
Top Plan Cost Per Month$By request$619

Paychex vs CheckMark Payroll Features

FeaturesPaychexCheckMark Payroll
Target Business SizeEnterpriseMid size business
Unlimited Payrolls✘✔
Automated Tax Filing & Payments✔✔
E-sign I-9 & W-4✘✘
Live Customer Support✘✔
Third-Party Integrations✔✔
Ability To Manage Employee Benefits✔✔
Employee Access To Platform✔✔
Direct Deposit✔✔
Expense Reimbursement✘✔
Time Off Accrual✔✔
Pre-Tax Deductions✔✔
Wage Garnishment✔✔
Background Checks✔✘
Check Printing✔✔
Check Delivery✔✘
API✔✘

Paychex Essentials Features

  • Payroll Processing
  • Taxpay® Payroll Tax Administration with W-2/1099
  • Employee Pay Options
  • Garnishment Payment Service
  • Employee Self-Service and Mobile Experience
  • Financial Wellness and Cashflow Assistance
  • Employee Onboarding
  • HR Library
  • Analytics and Reports Center
  • New Hire Reporting
  • Labor Posters

CheckMark Payroll CheckMark Payroll Pro Features

  • Self Service Payroll
  • Automatic Payroll Calculation
  • Unlimited Companies
  • Unlimited Salaried & Hourly Employees
  • Unlimited Payrolls (Regular, Bonus, Off-Cycle, etc.)
  • All Pay Frequencies
  • Multiple Pay Rates
  • MICR Encoded Check Printing
  • ACH Direct Deposit
  • Printing & E-Filing of Forms 941, 940, 944, 943, W-2, & W-3
  • Employer Payroll Tax Filings
  • Access to 40+ Types of Payroll Reports
  • Employee Benefits (Health, Retirement, Insurance, etc.)
  • Customized Vacation and Sick Leave Policies
  • Customized Deductions and Garnishments
  • Up to 90 mins within 12 months
  • Online access to program fixes

Paychex Pro Features

  • Payroll Processing
  • Taxpay® Payroll Tax Administration with W-2/1099
  • Employee Pay Options
  • Garnishment Payment Service
  • General Ledger Service
  • Employee Self-Service and Mobile Experience
  • Financial Wellness and Cashflow Assistance
  • Learning Management System1
  • Employee Onboarding
  • HR Library
  • Employee Handbook Builder
  • Pre-Employment Screening
  • Analytics and Reports Center
  • New Hire Reporting
  • Labor Posters
  • State Unemployment Insurance Service
  • Workers’ Compensation Payment Service2 or Report Service
  • General Ledger Integrations

CheckMark Payroll CheckMark Payroll Pro+ Features

  • Self Service Payroll
  • Automatic Payroll Calculation
  • Unlimited Companies
  • Unlimited Salaried & Hourly Employees
  • Unlimited Payrolls (Regular, Bonus, Off-Cycle, etc.)
  • All Pay Frequencies
  • Multiple Pay Rates
  • MICR Encoded Check Printing
  • ACH Direct Deposit
  • Printing & E-Filing of Forms 941, 940, 944, 943, W-2, & W-3
  • Employer Payroll Tax Filings
  • Access to 40+ Types of Payroll Reports
  • Employee Benefits (Health, Retirement, Insurance, etc.)
  • Customized Vacation and Sick Leave Policies
  • Customized Deductions and Garnishments
  • Up to 300 mins of support within 12 months
  • Exclusive Pro+ toll-free phone number
  • Top-of-the-queue priority
  • Reduced data recovery rates
  • Online access to program fixes
  • Exclusive Pro+ Support Live Chat

Paychex vs CheckMark Payroll Pro & Cons

PaychexCheckMark Payroll
Pros
  • User Friendly
  • Saves Time
  • Customer Service
  • Reporting
  • Easy Processes
  • Direct deposit option
  • Easy to use and interfaces with CheckMark’s Accounting program, MultiLedger
  • Automated reports
Cons
  • Not User Friendly
  • Technical Issues
  • Adjustment Issues
  • Slow
  • Customer Service
  • Technical support, glitches with Mac
  • High cost
  • More features like direct sms, email, other tax purpose forms

Other Payroll Software Comparisons

  • PrimePay vs Paylocity
  • SumoPayroll vs Ready Pay by HR3
  • QuickBooks Payroll vs Razorpay
  • Fingercheck vs Xero Payroll
  • Rippling vs Greenshades
  • Papaya Global vs Checkwriters
  • Kashflow Payroll vs Proliant
  • Paycom vs EPAY Payroll
  • PayCaptain vs Trolley
  • OnPay vs TriNet

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