Published on Jun 25, 2025 5 min read

Top 8 Payroll Tools for Small Business Owners

Handling payroll is one of the most crucial yet time-consuming tasks small business owners face. Every detail—from calculating salaries to filing taxes—needs to be precise and timely. A single error could lead to tax penalties or dissatisfied employees. Therefore, choosing the right payroll system is essential.

These tools automate payments, tax filings, and employee records, taking the heavy lifting off your shoulders. They reduce errors, save time, and allow you to focus on growing your company. Whether you run a small retail store, a startup, or manage remote staff, there’s a payroll tool for you. This article highlights eight of the best payroll solutions that can streamline and simplify your payroll process.

Top 8 Payroll Tools for Small Business Owners

Below are the top payroll tools that can simplify your payroll tasks and save time for small business owners.

Gusto

Among the most reliable payroll software, Gusto is designed primarily for small businesses. It offers employee self-service portals, direct deposit, automatic tax filing, and full-service payroll. Gusto also provides benefits management and time tracking, making it a great choice for managing payroll and HR in one place. The user-friendly interface simplifies setup and is especially useful for remote teams. While it can be more costly if advanced features are needed, Gusto stands out for its accuracy, simplicity, and robust support system.

QuickBooks Payroll

QuickBooks Payroll is an excellent choice for those already using QuickBooks for accounting. It seamlessly integrates accounting and payroll data, allowing automated tax filings, same-day direct deposit, and quick payroll management. QuickBooks Payroll offers tax penalty protection in its higher-tier plans and 24/7 professional support. Its mobile access is a boon for business owners on the go. Although the cost may be higher for non-QuickBooks users, it is fast, secure, and ideal for companies seeking a comprehensive financial solution.

Patriot Payroll

Ideal for small businesses and startups, Patriot Payroll is an affordable and straightforward payroll software. It comes in two versions: basic payroll and full-service payroll. The basic plan requires you to handle taxes, while the full-service plan manages everything. Patriot offers a free setup, responsive customer service, and a user-friendly dashboard. Designed with small businesses in mind, it supports both 1099 contractors and W-2 employees. While it lacks extensive HR features, its low cost and simple design are appealing to budget-conscious business owners.

ADP RUN

ADP RUN is a powerful payroll solution for small businesses with fewer than 50 employees. Backed by ADP, a leader in HR and payroll, the program offers automated tax filing, payroll processing, and compliance alerts. It also provides mobile access and integrates well with popular HR and accounting systems. ADP RUN offers numerous options for insurance, employee benefits, and retirement plans. Though pricing isn’t displayed on the website, you can request a quote based on your needs, allowing flexibility as your team grows. It’s perfect for companies seeking a reliable, well-established provider.

OnPay

OnPay is an easy-to-use and affordable payroll software for small businesses, nonprofits, and farms. It covers tax filings and full-service payroll, supporting both contractors and employees. OnPay allows unlimited monthly payroll runs without additional fees and includes standard HR tools like document storage and employee onboarding. New users will find the platform intuitive due to its clean design and free setup assistance. While it lacks a mobile app, the website functions well on mobile devices.

Paychex Flex

Paychex Flex is a versatile payroll and HR tool beneficial for small and growing businesses. It offers time tracking, benefits administration, automatic tax filing, and full-service payroll processing. Paychex Flex’s add-ons let you customize the service to fit your needs, supporting various pay schedules and providing an employee self-service portal. The platform offers 24/7 customer support. Although its extensive features may initially seem complex, particularly for very small businesses, it’s ideal for those planning to grow. Strong security and scalable solutions make Paychex Flex a robust choice for long-term success.

Square Payroll

Square Payroll is ideal for businesses already using Square’s point-of-sale system, especially in retail or hospitality sectors. It offers direct deposit, tax filing, and full-service payroll with tip reporting. Square Payroll is effective for both employees and contractors, particularly part-time and hourly workers. The tool’s seamless integration with Square’s sales data and time tracking greatly simplifies payroll processes. While it works best within the Square ecosystem and lacks some advanced HR features, its simplicity and mobile-friendly design make it an excellent choice. It’s reasonably priced and easy to set up, allowing multiple payment options with just a few clicks.

Wave Payroll

Wave Payroll is part of Wave’s suite of financial solutions tailored for small businesses. It’s ideal for small teams or sole proprietors. While Wave Accounting is free, Wave Payroll is a paid service offering affordable full-service payroll. It integrates seamlessly with Wave’s accounting and invoicing systems and supports tax filing in a few states. The platform’s simple interface is easy to use, supporting employee access and direct deposit. Despite limited availability and lacking advanced features, it’s a great low-cost option for straightforward payroll needs.

Conclusion

For small business owners, choosing the right payroll tool can make a significant impact. It ensures compliance, saves time, and helps avoid costly errors. Whether your needs are simple payroll operations or full HR support, there is a solution that fits your demands and budget. Tools like Gusto, QuickBooks Payroll, and Patriot offer robust capabilities without unnecessary complexity. Each option here is designed to simplify payroll and enhance accuracy. Take the time to explore and compare them. Having the right tool will enable you to focus more on your business and less on paperwork.