8 Best Payroll Software for Small Business (2026)

There’s nothing quite like the feeling of a paycheck hitting your bank account. As a small business owner, you can make that feeling happen. And the right payroll software helps you make sure that all your paychecks are accurate, timely, and perfectly organized. 

We’ve got a round-up of the best payroll software for small businesses in 2026, so you can find the system that delivers that first paycheck feeling every time.

🌟 KEY TAKEAWAYS

Reliable payroll software is key to improving accuracy, compliance, and morale.

Good payroll software should offer automation, flexibility, and tax compliance features.

FreshBooks payroll is the top pick for small business owners looking for robust, accurate, and scalable payroll software.

Why payroll software matters for small businesses

Payroll is an essential part of every business. When your payroll is on time, accurate, and efficient, it keeps morale high and compliance on track. Payroll software reduces the problems associated with manual payroll, like data-entry errors and compliance issues. It minimizes delays, boosts efficiency, and saves you time. This translates to a boost in employee satisfaction and retention. Accurate and prompt payroll supports employee trust, lifts morale, and improves IRS tax compliance. It’s a win for everyone on your team.

Top small business small payroll software

Looking for the best payroll software for your small business? Discover our top picks with our payroll all-star list.

Best for freelancers and small businesses

Our stand-out choice for the best overall payroll software for small businesses. 

FreshBooks Payroll

For small business owners who want simplicity, integration, and efficiency, FreshBooks payroll software is your go-to solution. FreshBooks P payroll, powered by Gusto, brings you the best of both worlds. You get unlimited payroll runs and automated tax filing and calculations with all the HR features of Gusto. Plus, it’s easy to scale so your payroll software can grow with you.

Best payroll for startups and local businesses

All the functions, none of the frills. These software options deliver efficient and accurate payroll for startups and local small businesses.

Gusto

Gusto is one of the top-rated HR platforms for small to medium businesses. An integrated payroll and HR management system makes it easy to manage payroll, health insurance, background checks, and new-hire information in one place. It only lets you serve employees in one state, and the basic plan doesn’t include scheduling or time tracking, so you’ll pay extra if you want to include these perks.

Wave Payroll

Wave shines in the payroll-adjacent features: invoicing and accounting integrations. The payroll functions themselves are fairly standard, although they don’t include unlimited payroll runs or HR functions. However, you’ll have access to a free invoice generator, free invoice templates, and Wave’s affordable accounting software.

Best payroll for multi-state and global businesses

These payroll software options deliver multi-state and international compliance and payroll features to take your business worldwide.

Remote

Remote’s biggest strength is that it can handle global payroll management. With features for almost 200 countries, you can make sure global employees are paid correctly, on time, and with the appropriate tax withholdings. But you’ll pay a comparatively higher monthly rate for these features. It also has limited payment flexibility, so direct deposit is only available for some countries.

OnPay

OnPay is popular with small business owners who are new to payroll software. It’s easy to set up and use, and it can track health benefits for all 50 states (great for companies that are national, but not global just yet).

Best payroll for scalable businesses

Want your payroll to go the extra mile? These software options include extra features for invoicing, accounting, and comprehensive business reports.

QuickBooks Payroll

For business owners who already use QuickBooks, the payroll feature offers a ton of integrations, like HR, accounting, and commissions. However, time tracking features are sold separately, which can drive up the cost of performing payroll runs. While QuickBooks does offer the option for multi-state filing, that comes at an extra fee, so the basic package is best for local businesses.

ADP Run

ADP is a major payroll provider with a wide range of HR solutions. They offer payroll options for smaller businesses and larger enterprises, with enterprise-friendly features like comprehensive reporting to support scalability. You can focus on everything from payroll liability to deductions and paid time off, giving you far more flexibility than standard reporting. The tradeoff is that ADP Run doesn’t offer unlimited payroll runs, and features like time and attendance need to be bought as add-ons.

Rippling

Rippling goes beyond the standard payroll software automations to include a robust system for creating your own automations. For example, if your company offers a bonus for referring new employees, Rippling lets you automate the process for faster, more accurate bonus tracking. The range of automations is great for saving time and reducing manual errors. However, if you want other features like HR, you’ll have to add those on for an additional cost.

Pricing: starting at $40/month plus $8 per employee

How payroll software works

How your payroll software works depends on the features and setup. In general, you can expect the following overall workflow:

Step 1: Input data

The first step is to input your employee data. This includes employee onboarding information like bank account details and social security numbers, as well as pay period data like hourly wages, salaries, and hours worked.

Step 2: Automated calculations

Next, your payroll software will automatically perform payroll calculations. It will calculate how much is owed to each employee for that pay period, as well as any relevant tax deductions.

Step 3: Tax compliance

Your payroll software will perform the necessary tax withholdings for local, state, and federal agencies. Automatically tracking this information also helps streamline your filing for tax time. 

Step 4: Wage payout

Finally, your payroll software will distribute the net pay to your employees. Depending on how you’ve set up your payment system, employees can receive their paychecks via direct deposit or check distribution.

These days, automated payroll is standard for managing your employee payments and tax filings. Small businesses can save hours every week by ditching the old spreadsheets and manual calculations and switching to a streamlined, automated system. Plus, no more delayed payments or paycheck mixups = happier employees.

What to look for in payroll software

Wondering how to choose and set up your payroll accounting software? When you’re shopping for the perfect fit, make sure your top pick includes these essential features:

While there are many free or low-budget online tools for automating payroll, they often only offer basic tools and can lack security features. Payroll involves a high degree of sensitive information, including bank details and employee social security numbers—making quality payroll software a worthwhile investment. It’s worth paying for quality payroll software that not only gets the job done right, but keeps you, your employees, and your business safe.

How FreshBooks payroll software makes payroll a breeze

Payroll software isn’t just a nice-to-have—it’s essential for small businesses that want to improve their efficiency and compliance. It can be the key to meeting your tax obligations and paying your employees on time, which also helps boost employee trust and company morale.
FreshBooks is a great all-around solution for improving your payroll. The automated tax filing and calculations keep you on top of your compliance responsibilities, while unlimited payroll runs and robust integrations keep staff paid and happy. Start your free FreshBooks trial today and discover how easy payroll can be.

Frequently Asked Questions

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