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

CheckMark Online Payroll is a simple and affordable cloud-based payroll software for small businesses, accountants, bookkeepers, CPAs, and payroll professionals. It brings together payroll calculations, direct deposit, paycheck printing, employee self-service, payroll reporting, and tax form preparation in one platform.

Payroll processing

Calculate employee wages, overtime, additional income, deductions, taxes, and net pay using configurable payroll settings. CheckMark Online Payroll supports unlimited employees and unlimited payroll runs. Users can configure pay categories for bonuses, commissions, and other earnings.

Employee payments

Prepare employee payments using ACH direct deposit files or printed MICR-encoded checks. ACH files can be submitted to the business’s bank or ACH provider. Users can also email pay stubs.

Employee self-service

The Employee Self-Service portal allows employees to access pay stubs, W-2 forms, leave balances, attendance information, personal details, and available documents online.

Deductions, benefits, and time off

Configure payroll deductions and benefits, including applicable 401(k) and Roth 401(k) contributions, employer matching, garnishments, and other deduction types. Track paid time off (PTO) and maintain leave balances for categories such as sick time and vacation.

Payroll tax reporting and reports

CheckMark Online Payroll provides tools for preparing supported federal payroll tax forms, including Forms 941, 940, 943, and 944, as well as year-end W-2 and W-3 wage reporting. More than 40 payroll reports help users review wages, liabilities, and other payroll data. Reports can be viewed, printed, or exported in supported formats.

Key features and benefits

• Unlimited payroll runs for flexible payroll scheduling.

• Payroll calculations for wages, overtime, earnings, deductions, taxes, and net pay.

• ACH file generation for direct deposit through a bank or ACH provider, plus MICR paycheck printing.

• Employee Self-Service for online access to pay stubs, W-2 forms, leave balances, and personal information.

• Payroll deduction and benefit settings for supported retirement contributions, employer matching, and garnishments.

• PTO tracking and employee document management.

• Payroll tax reporting, year-end wage forms, and more than 40 payroll reports.

Editions for different needs

Business Edition is designed for businesses managing payroll for a single company. It provides online tools for calculating employee pay, preparing payments, managing deductions, and handling payroll reporting.

Accountant Edition is designed for accountants, bookkeepers, CPAs, and payroll professionals who manage payroll for multiple companies or clients. It supports multi-company payroll management, helping professionals organize payroll work across client businesses.

CheckMark Online Payroll is a practical option for organizations looking for affordable online payroll software with essential tools for employee payments, payroll administration, tax reporting, and employee records. The editions serve both single businesses and professionals managing client payroll.