CheckMark Payroll Software - 2026 Pricing, Features, Reviews & Alternatives

CheckMark Payroll Software is simple and affordable payroll software for small businesses and accountants. Our DIY, in-house payroll software helps you process payroll, pay employees, manage payroll records, and prepare W-2 filings in one place. Compatible with the latest versions of Windows and macOS, CheckMark gives you the flexibility to manage payroll in-house and maintain control over the process.

With CheckMark, you can set up multiple companies, add unlimited employees, and run unlimited payrolls. Process each pay period using regular hours, additional income, tax withholdings, and deductions. Pay employees by ACH direct deposit or print MICR checks using blank or pre-printed check stock. You can also email PDF pay stubs to employees who receive direct deposits.

CheckMark lets you set up payroll to match the way your business works. Customize income and deduction categories, pay periods, pay frequencies, PTO, and other payroll settings for each company. Create additional income categories and assign the categories you need to individual employees. The software also supports deductions such as 401(k) contributions and employer matches.

To make payroll processing easier, CheckMark can import employee hours from a time clock or spreadsheet. Track accrued sick and vacation time and use those hours when calculating payroll. The software also maintains federal and state withholding tables to help calculate payroll taxes.

CheckMark supports common payroll tax and reporting requirements. Print or e-file W-2 and W-3 forms with the Social Security Administration (SSA) and file required forms with most states. The software also supports payroll tax forms such as Forms 941, 940, 943, and 944. For direct deposit, CheckMark creates ACH-formatted files that you can submit through your bank or a cloud-based deposit service.

Use CheckMark Payroll Software as a standalone desktop solution or integrate it with other accounting software, including QuickBooks and CheckMark MultiLedger. Whether you process payroll for one company or manage payroll for multiple companies, CheckMark gives you the tools to run payroll in-house on Windows or macOS.