Best Payroll Software for Small Businesses & CPAs.

What is payroll software?

Payroll software is a desktop or browser-based application that automates the process of calculating employee wages, withholding taxes, processing deductions, generating paychecks or direct deposit payments, and producing the tax forms required for IRS and state compliance. It handles the full payroll lifecycle, from entering employee hours through to year-end W-2 filing. Payroll software is used by business owners, HR managers, accountants, bookkeepers, and payroll professionals managing payroll for businesses of any size.

What is the difference between desktop and online payroll software?

Desktop payroll software is installed directly on your Windows or Mac computer. Your payroll data is stored locally on your computer; no cloud server holds it. It gives you full control over your data. Online payroll software runs in a web browser and stores data on secure remote servers. It can be accessed from any device with an internet connection. Both handle the same core payroll functions; the difference is where your data lives and how you access it. CheckMark offers both: see Desktop Payroll Software and Online Payroll Software for full details.

What is cloud-based payroll software?

Cloud-based payroll software (also called online payroll software) is accessed through a web browser rather than a locally installed application. Employee data and payroll records are stored on secure remote servers, allowing you to run payroll from any device, desktop, laptop, tablet, or smartphone, from any location. Cloud-based payroll typically includes features like automated payroll processing, real-time access for multiple users, and employee self-service portals. CheckMark Online Payroll is a full-featured cloud payroll software solution.

How much does payroll software cost?

CheckMark Payroll Software starts at $579 for the first year for the Pro plan, a flat annual fee that covers unlimited employees and unlimited payroll runs. There are no per-employee monthly charges, no add-on fees for direct deposit or W-2 filing, and no surprise costs. CheckMark is affordable payroll software for small business because your cost stays fixed as your team grows.

See full pricing

CheckMark Online Payroll offers straightforward and affordable pricing with a $20.00 base fee plus $5.00 per employee. This plan includes a single company setup, unlimited payroll runs, an employee self-service portal, and document management, giving you all the essential tools needed to manage payroll efficiently without hidden costs.

What payroll software works on Mac?

Most payroll software are Windows-only or browser-based. CheckMark Payroll Software is one of the only payroll software solutions with a native macOS application, built for Mac since the 1980s, when CheckMark pioneered payroll software on the Apple platform. It runs natively on current macOS versions with full feature parity with the Windows version. If you need payroll software for Mac, CheckMark Payroll Software is specifically designed for you.

Do I need payroll software for my small business?

Yes. Manually calculating payroll, wages, tax withholdings, deductions, employer taxes, and year-end forms is error-prone and time-consuming. IRS penalties for payroll errors and late filings can exceed $1,000 per incident. Payroll software automates the calculations, keeps your tax tables current, generates the forms you need to file, and produces the records required if you face an audit. For small business owners without a dedicated payroll department, CheckMark is designed to make payroll processing straightforward and accurate without requiring payroll expertise.

What features should I look for in payroll software?

The most important features for small business payroll software are:

• Automated payroll tax calculations for federal, state, and local taxes
• Direct deposit via ACH
• Year-end W-2 filing
• Support for multiple pay frequencies
• Detailed payroll reports for accounting and auditing
• Integration with your accounting software
• Reliable, accessible US-based customer support

CheckMark includes all of these in every plan.

Can payroll software file taxes automatically?

CheckMark generates all required tax forms (941, 940, W-2, W-3, and state forms) with pre-filled data from your payroll records, which you then file yourself or give to your accountant.

Is my payroll data secure?

Yes, though the security model differs between products. CheckMark Desktop Payroll stores all payroll data encrypted on your local computer only. No cloud server, no third-party storage, no external exposure. CheckMark does not access or retain your payroll records. CheckMark Online Payroll stores data on secure cloud servers with encryption in transit and at rest, with access controlled by secure login credentials. In both cases, your payroll data is protected against unauthorized access. For maximum data privacy, desktop payroll software keeps everything under your direct control.

Can I switch to CheckMark from another payroll provider?

Yes. You can import existing payroll data into CheckMark from ADP, Paychex, Gusto, QuickBooks Payroll, Rippling, Deel, Square Payroll, OnPay, SurePayroll, Paycom, Paylocity, Workday, Dayforce (Ceridian), Patriot Payroll, Papaya Global, Remote Payroll, Justworks, Homebase, TimeTrex, Insperity, or any provider that exports data in .csv or .txt format. Our payroll setup support team will help you enter year-to-date payroll totals and get your first payroll run completed correctly. You can switch at any point in the year, not just at year-end. Start with a free trial and let us walk you through the migration.

Does CheckMark support 1099 independent contractors?

CheckMark handles W-2 employee payroll. For 1099 independent contractors, CheckMark offers a separate 1099 software product that prepares, prints, and e-files 1099-NEC, 1099-MISC, and related forms. If you pay a mix of W-2 employees and 1099 contractors, the two products work together.

Can I manage payroll for multiple companies?

Yes. CheckMark supports multiple company files, making it a practical choice for accountants and bookkeepers managing payroll for several clients. In the desktop software, the base license covers one company; additional company licenses are available at tiered pricing. In Online Payroll, you can subscribe to a new subscription, which is offered at a discounted price.

What size businesses can use CheckMark?

CheckMark handles businesses from 2 employees to 2,000+ employees, with no price difference between them. The flat annual fee model means a startup processing payroll for 3 people pays the same as a mid-sized business running payroll for 300. The software is in use across every major US industry, from sole proprietors running their first hire to established businesses with complex multi-department payroll structures.

Is there a free trial?

Yes. CheckMark Payroll Software offers a full-featured 60-day free trial, and CheckMark Online Payroll also offers a 14-day free trial, both with no credit card required. You get access to all software features and can process real payroll runs during the trial period. If you’re switching from another provider, our setup support team will help you import your employee data and year-to-date payroll so you can evaluate the software using your actual payroll.