Best Payroll Software: Top Picks for Small Businesses in 2025

Let's face it—payroll processing isn't just about cutting checks. It's about getting things right, staying compliant, and saving time—three areas where many small businesses struggle. 

According to ADP's report "The Potential of Payroll in 2024" the global accuracy level for payroll is just 78%. Plus, our 2023 survey reveals that on average, employers spend 63 hours each year running payroll and 76% of employers have made a payroll calculation error in the past. 

That's over a week and a half of work hours devoted to payroll, with most businesses still making mistakes. Finding the best payroll software isn't just convenient—it's essential for your business's financial health. 

Our payroll software comparison cuts through the noise. We'll help you find the perfect payroll system to keep errors in check, take the paperwork off your plate, and pay your team on time without the stress.

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10 best payroll software for small businesses: Top rated payroll software for 2025

Finding the best payroll service for small business needs can help you stay accurate and compliant every payroll run. Here are our top ten picks in 2025:

1. Homebase

Best for: Small businesses needing an all-in-one solution for payroll, time tracking, and HR.

When comparing popular payroll systems, Homebase stands out as the best payroll software small business owners can rely on in 2025.

All your payroll info in one place

Homebase puts all your employee information in one place. Store and access employee data instantly, update records with a click, and say goodbye to digging through files or spreadsheets when it's time to run payroll.

Run payroll without the math

Time tracking is connected to your payroll process—meaning Homebase automatically captures hours, breaks, overtime, and PTO. We feed that data directly into your payroll management system. No manual entry means fewer mistakes and faster processing.

End the compliance chaos

With Homebase, you won’t need to stress about tax compliance. We handle federal, state, and local tax calculations with automated tax filings. No more wondering if you've missed a deadline or calculated something incorrectly—we've got you covered.

Don’t just hear from us—here’s what our customers have to say about Homebase’s payroll services: 

“Homebase Payroll makes me feel confident that I’m doing things correctly—and it’s been a huge timesaver. I enjoy the reminders, the ease of use, and the peace of mind knowing that all of my quarterly and biweekly payroll responsibilities are handled automatically. It’s like having my own personal assistant.” – Caprice, owner of Southern Speech

“I honestly have not thought about payroll since switching to Homebase—which is the best endorsement I can give a platform designed to make you more efficient or take away a once tedious task. WE LOVE IT.” – Eric, owner of The Gear Attic

Key features:

• Integrated time tracking and scheduling
• Automatic tax calculations and filings
• Direct deposit and digital paystubs
• New hire reporting
• PTO tracking and management
• Employee self-service portal

Pricing: Starts at $39/month + $6 per active employee.

Tired of juggling payroll, time tracking, and HR? Start using Homebase today and take the hassle out of managing your team! Contact us for a free walkthrough of our payroll services.

2. Gusto

Best for: Growing businesses that need scalable HR, payroll tools, and benefits management.

Gusto consistently earns high marks among top payroll software for its user-friendly interface. It makes payroll accessible for users at any tech skill level—no accounting degree required. 

Pros

The platform streamlines employee information management and connects smoothly with HR functions, creating a more efficient workflow for growing teams.

It handles tax calculations and filings, keeping you compliant with changing regulations. Gusto also automatically tracks hours and attendance, minimizing the chance of human error. That means your payroll calculations are way more accurate.

Cons

The downside? Some users mention that customer support can be slow to respond when issues arise. And while Gusto works beautifully for small to mid-sized businesses, it may not scale as effectively for larger organizations with complex needs.

Key features:

• Full-service payroll processing
• Benefits administration
• Time tracking
• Tax filing and compliance
• Employee self-service portal

Pricing: Tiered plans for different business sizes, starting with the Simple tier at $40 per month + $6 per employee.

3. QuickBooks Payroll

Best for: Businesses already using QuickBooks for accounting, managing payroll, and bookkeeping for payroll expenses.

In any comparison of payroll software, QuickBooks Payroll stands out as comprehensive payroll processing software that integrates seamlessly with QuickBooks accounting software. 

Pros

If you're already using QuickBooks for your books, this payroll solution creates a match made in efficiency heaven. Employee data management becomes simpler, and time tracking happens automatically without jumping between systems.

This HR and payroll software handles tax calculations with precision and delivers timely payments through direct deposit—including a same-day direct deposit option that many competitors don't offer. 

Cons

While the tax compliance features work reliably, some users find the overall package relatively expensive, especially for smaller operations. And if you're not using QuickBooks for accounting, this integration might be overkill for your needs.

Key features:

• Same-day direct deposit
• Automated tax calculations and forms
• Integration with QuickBooks accounting
• Mobile payroll management
• Automated payroll runs

Pricing: Tiered plans, starting with the Core tier at $42.50 per month + $6 per employee. Discount available when bundled with QuickBooks.

4. ADP

Best for: Mid-sized to large businesses needing enterprise-level payroll features.

ADP is the veteran player among top payroll systems, known for scalability that fits businesses from small shops to major corporations. 

Pros

It efficiently manages employee information and automates time tracking to streamline your payroll tasks. Tax calculations and filings happen with precision, and the system stays current with constantly changing regulations.

As one of the most established payroll software providers for small businesses, ADP offers comprehensive reporting options and global capabilities that make it attractive for growing companies with big ambitions. 

Cons

The drawbacks? Users report inconsistent customer service experiences—sometimes excellent, sometimes frustrating. And the cost structure can feel prohibitive for smaller businesses just starting out. 

Key features:

• Global payroll capabilities
• Advanced HR and compliance tools
• Benefits administration
• Talent management
• Extensive reporting options

Pricing: Custom quotes based on business size.

5. Paychex

Best for: Businesses needing comprehensive HR and payroll services.

Among popular payroll software options, Paychex stands out from other payroll software options by being a payroll management software with a bunch of extra service offerings—like 24/7 customer support. 

Pros

The automatic time and attendance tracking removes the headache of manual timesheet review, while tax calculation tools keep you compliant with changing regulations—taking the paperwork off your plate.

Another major selling point is Paychex's 24/7 customer support—a rare find in the payroll world where most competitors offer limited support hours. 

Cons

The downsides? Paychex can stretch the budget for very small businesses, and customer support quality receives mixed reviews. Some users find the abundance of features overwhelming when they just need simple payroll software.

Key features:

• 24/7 customer support
• Tax credit services
• Workers' compensation reporting
• HR advisory services
• Multiple payment options

Pricing: Contact sales to get a quote.

6. Square Payroll

Best for: Retail and restaurant businesses using Square POS.

If you're already using Square's point-of-sale system, then Square Payroll might be the best fit for you. 

Pros

As small business payroll software, Square keeps pricing crystal clear with no sneaky long-term contracts. The user-friendly mobile app lets you approve timecards and run payroll from anywhere—perfect for busy restaurant owners or retailers who rarely sit at a desk. 

The seamless integration lets time tracking data flow directly into payroll—no double entry, fewer headaches, and fewer errors. The system automatically handles tax filings at all levels, taking a huge burden off your plate—especially if you're working with hourly employees or contractors. 

Cons

Just watch out for occasional hiccups with tax calculations—particularly state and local withholdings—where the system sometimes gets things wrong.

Key features:

• Seamless integration with Square POS
• Automatic tax filing
• Time tracking integration
• Contractor-only pricing option
• Pay employees and contractors

Pricing: $35/month plus $5/employee per month (full-service plan); $5/month per contractor (contractor-only plan)

7. OnPay

Best for: Small businesses looking for straightforward, all-inclusive pricing.

Looking for a transparent, all-inclusive pricing model with no frills? OnPay is a payroll software provider that does just that. 

Pros

OnPay packs robust HR tools into its platform, including customizable onboarding workflows, document storage, automated tax filings and payments—including those dreaded year-end forms and new hire reporting that often trip up small businesses. 

The clean, simple interface and unlimited payroll runs make it perfect for businesses without a dedicated payroll specialist on staff. 

Cons

Worth noting: a handful of customers have experienced missed tax deadlines resulting in penalties—something to keep an eye on if you choose this platform.

Key features:

• All-inclusive pricing
• Agricultural and nonprofit specialization
• Custom user permissions
• Employee self-onboarding
• Integrated HR tools

Pricing: $40/month plus $6/employee per month.

8. Wave Financial

Best for: Budget-conscious small businesses using Wave's free accounting software.

In the world of top payroll systems, Wave Financial is an affordable payroll program for small business users, and it's the perfect companion to Wave's free accounting software. 

Pros

Wave Financial handles the essentials: running payroll, calculating taxes, and generating necessary reports. The software comes in two flavors—self-serve and tax service states—with pricing that reflects the level of tax support provided. 

For very small businesses or those just starting out, Wave offers a wallet-friendly entry point into automated payroll without unnecessary frills.

Cons 

One thing to consider? Their payment processing service occasionally freezes accounts during verification processes, which can be frustrating if you're caught off guard.

Key features:

• Integration with Wave's free accounting
• Self-service employee portal
• Direct deposit or check printing
• Year-end tax forms
• Automated journal entries

Pricing: Free plan available. Paid plan costs $16/month billed monthly or $175/year billed annually.

9. Rippling

Best for: Tech-forward companies looking for advanced automation and integrations.

Rippling takes a unique approach, offering an HR payroll software focusing on deep integration across all your business systems. 

Pros

It sets itself apart with lightning-fast processing—payroll can be run in just 90 seconds—and automates workflows across HR, IT, and finance by connecting your workforce data seamlessly.

The platform's standout feature is its ability to manage global payroll in over 50 countries, making it ideal for businesses with international teams or expansion plans. 

Cons

It's a bit pricier than more basic payroll solutions. But if you're a tech-savvy business, Rippling's powerful automation capabilities may be worth the price because of the time you save. 

Key features:

• Global payroll capabilities
• 500+ app integrations
• Device management
• Workflow automation
• Advanced reporting and analytics

Pricing: Contact sales to get a quote.

10. Patriot Payroll Software

Best for: Budget-conscious small businesses seeking affordable, straightforward payroll.

Patriot Software is a payroll management system that delivers core payroll functions at some of the lowest prices on the market without sacrificing essentials. 

Pros

What makes Patriot unique is its flexible approach that lets you choose between handling your own tax filings (Basic) or opting for full-service tax filing (Full Service). This modular design means you only pay for exactly what you need. 

The platform offers a remarkably intuitive interface that even complete payroll beginners can navigate with confidence, plus free expert setup assistance to ensure you start on the right foot.

Cons

But if you're looking to expand your business to other countries or if your team likes working on mobile, Patriot Software may be a hard sell with no mobile app or support for international payroll.

Key features:

• Affordable pricing with transparent structure
• Free setup and US-based support
• Unlimited payroll runs
• Employee self-service portal
• Flexible tax filing options

Pricing: Basic starts at $17/month plus $4/employee; Full Service starts at $37/month plus $5/employee.

Key benefits of using payroll software

Are you still wondering, "Is payroll software really worth it?" Here's how the right payroll app can transform your business operations and save you serious headaches.

Saves time & eliminates manual calculations

Instead of spending hours crunching numbers, you can run payroll in minutes. Top payroll systems automate calculations and eliminate manual data entry. Need reports for your accountant or business planning? Generate them with a click.

Here's a reality check: Deloitte found that more than 25% of payroll staff spend most of their time just running payroll and handling manual tasks. Imagine what your team could accomplish if you gave them that time back.

Ensures tax compliance & accuracy

Tax mistakes can be costly—and they're easy to make when calculating manually. Most popular payroll software reduce these errors by automating tax calculations. The software keeps up with changing tax laws at federal, state, and local levels, so you don't have to.

With 61% of businesses naming legal and regulatory compliance as their biggest challenge, having software that handles tax requirements automatically removes a huge weight from your shoulders. No more tax-season panic or wondering if you've missed something important.

Improves security & prevents payroll fraud

Your employees' financial data is sensitive. Quality payroll system software offers bank-level security features to protect this information. 

Access controls ensure only authorized people can view or change payroll data, while regular backups prevent data loss. These security measures help maintain employee trust and shield your business from potential data breaches or fraud.

Offers employee self-service & direct deposits

Modern payroll apps put power in your employees' hands. Self-service portals let team members access pay stubs, update personal information, and check tax documents without bugging HR. 

This independence not only reduces your workload but also gives employees the instant access they expect in today's digital world. Plus, direct deposit features mean no more printing, signing, and distributing paper checks—saving time for everyone.

Deloitte's research shows that while most businesses are generally satisfied with their current payroll providers, self-service capabilities rank as the third most important area needing improvement (cited by 66% of respondents), right behind compliance and accuracy. 

That means implementing strong self-service features isn't just a nice-to-have anymore—it's a key factor in overall payroll satisfaction.

Types of payroll software: Which one is right for you?

Not all payroll solutions are created equal. Understanding the different payroll software options helps you pick what truly fits your business style and needs.

Cloud-based payroll software

Cloud payroll software lets you run payroll from anywhere with an internet connection—your office, home, or favorite coffee shop. Cloud-based systems update automatically, so you always have the latest tax tables and compliance features without lifting a finger. 

Also, your data backs up continuously, so there's no risk of losing important information if your computer crashes.

For growing businesses, cloud payroll software scales effortlessly—just add users or features as you need them. Most popular payroll systems now use cloud technology because it offers the best combination of convenience, security, and affordability for small businesses.

On-premise payroll software

Some businesses prefer keeping everything in-house. On-premise payroll software installs directly on your company's computers, giving you complete control over your data security since sensitive information stays within your network.

The trade-off? Higher upfront costs for hardware and software licenses, plus ongoing maintenance. Your IT team becomes responsible for updates, backups, and troubleshooting. 

While on-premise solutions offer top-notch security, they lack the flexibility and ease of cloud-based options.

Payroll software integrated with HR systems

Why stop at just payroll? Integrated HR and payroll software combines payroll with other HR functions like benefits administration, onboarding, and performance reviews. Enter information once, and it flows throughout your system.

Though they cost more than standalone payroll software for small business users, the efficiency gains and error reduction often make integrated systems worth the investment for businesses with more than a handful of employees.

How to choose the best payroll software for your business

Feeling overwhelmed by all the options? Don't worry—finding the right payroll software for your small business doesn't have to be complicated. Follow these steps to choose payroll management software that works for your business.

Step 1: Assess your payroll needs.

First things first—what does your business actually need? A solo entrepreneur has very different requirements than a company with 50 employees. Consider:

• How many employees do you have?
• How often do you run payroll?
• Do you need direct deposit?
• What tax filing support do you require?
• Do you have hourly workers, salaried staff, or contractors?
• Any industry-specific needs (like tip reporting or multiple job rates)?

Be honest about what features you'll actually use—don't pay for bells and whistles you'll never touch.

Step 2: Compare payroll software options.

Now it's time to see what's the best payroll software for your specific needs. Look at:

• Pricing structure—is it a flat fee or per-employee pricing?
• Core features vs. nice-to-have additions
• User interface—is it intuitive or confusing?
• Mobile app availability and functionality
• Customer support hours and communication channels
• Setup assistance and training resources

Remember that cheapest isn't always best—consider the value of your time and the cost of potential errors when evaluating online payroll providers.

Step 3: Check integrations.

Your payroll management system shouldn't be an island. Check that it plays nice with your:

• Accounting software.
• Time tracking tools.
• POS system (if applicable).
• Banking platform.
• HR and benefits systems.

Good payroll integrations eliminate double data entry and reduce errors. Ask specific questions about how data flows between systems—vague promises of "integration" often disappoint in practice.

Step 4: Read customer reviews.

What do actual users say about the top rated payroll software you're considering? Focus on reviews from businesses similar to yours in size and industry. Look for comments about:

• Reliability during tax season.
• Ease of correcting mistakes.
• Quality of customer support when problems arise.
• How well the software handles unique situations.

Pay more attention to recent reviews, as software can change significantly over time.

Step 5: Consider a free trial.

Never commit without testing the payroll processing software yourself. During your trial:

• Run a sample payroll with real data.
• Test the tax calculation features.
• Try the mobile app functionality.
• Contact customer support with questions.
• Have other team members test the interface.

Pay attention to your gut feeling—if something feels confusing or frustrating during the honeymoon period of a free trial, it won't get better after purchase.

Final thoughts: Choosing the best payroll software for your small business

From all-in-one systems like Homebase to more specialized payroll software solutions, your options for 2025 really depend on the exact payroll problem you're trying to solve. 

Whether you're looking for a payroll system that lets you pay your team accurately and on time, cut down on the math and paperwork, or keep your business tax compliant (or all of the above!) will ultimately determine what software you choose. 

If you're ready to simplify your payroll with software that can do it all—and take the hassle out of scheduling and time tracking, too—consider Homebase. 

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FAQs

What is the best free payroll software for small businesses?

Truly free small business payroll software options with complete features are rare. Wave Payroll comes closest when paired with Wave's free accounting software. 

Homebase offers free scheduling and time tracking that handles part of the process, making manual payroll calculations less painful. Most "free" options sacrifice essential features or require upgrading for tax filing support.

What is the best payroll software for small businesses?

Among the most popular payroll software options, Homebase earns our top recommendation for small business payroll needs. It combines user-friendly design with powerful time tracking integration and competitive pricing. 

For ultra-simple needs, Square Payroll offers straightforward pricing, while Gusto provides strong HR features. The best fit depends on your specific employee count, industry, and existing tools.

How much does payroll software cost?

Most payroll software for small businesses charges a monthly base fee (starting from $16) plus a per-employee fee (starting from $2). Small businesses typically pay $40-$100 monthly plus per-employee charges. 

When comparing payroll software, consider the total value—time saved and error reduction—not just the price tag. Most online payroll providers offer tiered plans with more features at higher price points.

How does payroll software work?

Popular payroll systems automate your entire payroll process. The payroll management software collects hours, rates, and deductions data, then calculates gross pay, taxes, and withholdings using current tax tables. 

The system processes payments via direct deposit or checks while maintaining compliance records and generating reports. Modern payroll apps integrate with time tracking and accounting systems for seamless data flow.

Does payroll software handle taxes?

Yes! Quality payroll systems for small businesses automatically calculate tax withholdings and many handle filings and payments—including quarterly forms, W-2s, 1099s, and new hire reporting. 

Full-service payroll providers for small businesses typically offer tax guarantees, covering penalties if their software makes mistakes. Always verify which tax services your specific plan includes.

Can I run payroll manually?

Technically yes, but it's risky and time-consuming. Manual payroll means calculating wages and taxes, processing deductions, generating checks, maintaining records, filing forms, and staying current on changing tax laws. 

Even one mistake can trigger penalties or compliance issues. For most small businesses, payroll solutions deliver reliability and efficiency that easily justify their cost.

What payroll software integrates with QuickBooks?

QuickBooks Payroll offers the tightest integration, but many other best payroll companies also connect well, including Gusto, ADP, Paychex, and OnPay. 

Look for features like automatic journal entries, tax payment recording, and mid-year switching capabilities. Most online payroll company providers demonstrate how their QuickBooks integration works, helping you find the best payroll service for your workflow.