Best Payroll Software for Small Business in 2025

Payroll takes up way more time than it should. You're manually adding up hours. Double-checking tax withholdings. Hoping you didn't mess up overtime calculations. And when something goes wrong? Your employees notice immediately.

The risks aren't small either. Tax mistakes trigger penalties. Calculation errors damage trust. And you're spending hours every pay period on work that payroll programs can handle automatically.

The best payroll software does the math for you. It files your taxes. It pays your team on time. You stop spending Sunday evenings with a calculator and start knowing everything's handled correctly.

This guide compares top payroll systems for 2025—pricing, features, and which one actually fits your business. Whether you have 5 employees or 50, hourly workers or salaried staff, we'll help you find company payroll software that works.

Let's fix your payroll process.

‍

{{banner-cta}}

‍

Best payroll software for small business: Quick comparison

Looking for payroll software that won't waste your time? Here's what works for small businesses.

Top payroll software picks:

• Homebase: Combines scheduling, time tracking, and payroll in one system built for hourly teams.
• Gusto: Solid choice when you're scaling up and need HR features alongside payroll.
• QuickBooks Payroll: Makes sense if QuickBooks already handles your books.
• Square Payroll: Works well when Square runs your payments and POS.
• ADP RUN: Built for businesses planning serious growth without switching systems later.
• Rippling: Connects 600+ apps if you want maximum automation across everything.

What matters most:

• Automatic tax filing at federal, state, and local levels.
• Direct time-to-payroll flow without manual data entry.
• Employee self-service so your team stops asking about their paychecks.

The difference? Most popular payroll systems handle the basics fine. The real question: are you juggling three separate tools or using one system that does it all? For hourly teams, Homebase combines everything.

Top payroll systems compared

Comparing payroll software saves you from expensive mistakes. Here's what you need to know.

Payroll software pricing tiers

Budget tier ($17-$35/month base):

• Patriot Payroll: $17/month + $4/employee.
• Square Payroll: $35/month + $6/employee.

Running a micro-business with under 10 employees? Per-employee costs add up fast. Five employees at $6 each versus $4? That's $120 yearly—enough to matter when every dollar counts.

Mid-range ($39-$60/month base):

• Homebase: $39/month + $6/employee.
• Gusto: $49/month + $6/employee.
• OnPay: $49/month + $6/employee.
• QuickBooks Payroll Core: $30/month + $5/employee.

Small to medium teams need tax automation, solid integrations, and room to grow. Don't buy payroll software that breaks when you hit twenty employees.

Enterprise (custom pricing):

• ADP RUN: Custom quotes.
• Paychex: Custom quotes.
• Rippling: Custom quotes.

Managing larger teams or complex multi-state payroll? Custom pricing gets you dedicated support, serious reporting tools, and compliance protection that prevents costly mistakes.

Best payroll software by key strength

Automation leaders:

• Rippling (600+ integrations, fast processing).
• Homebase (time-to-payroll automation).
• Gusto (tax filing automation).

Integration powerhouses:

• Rippling (600+ apps across HR, IT, finance).
• QuickBooks Payroll (native accounting integration).
• Homebase (scheduling + time tracking built-in).

Best for hourly teams:

• Homebase (tip management, shift scheduling).
• Square Payroll (POS integration for restaurants/retail).

Best for accountants:

• QuickBooks Payroll (client management features).
• ADP (multi-client dashboards).

Best payroll services and systems for 2025

Looking for payroll software examples? Here's what actually works, with real pricing and honest breakdowns of the best payroll systems.

Homebase: Best payroll software for hourly teams

Starting price: $39/month + $6/employee

Best for: Small businesses with hourly workers who need scheduling, time tracking, and payroll in one system.

What it does: Hours flow straight from time clock to paycheck without touching a spreadsheet. No more copying numbers between three different systems and hoping you didn't miss anything. Homebase handles tips, multiple pay rates, and PTO tracking from your phone.

Real customer experience: 

"Before Homebase I was manually tallying up my team's work hours and entering them into payroll, crossing my fingers I hadn't made any mistakes. Now our entire team logs in and out quickly and easily with the Homebase app, and all I have to do is send their hours to my payroll program with the click of a button. Time tracking for small businesses doesn't get better (or more affordable) than this!" — Kathleen Smith, Founder, Smiling Tree Toys

What you get:

• Stop copying hours manually—timesheets convert to paychecks automatically.
• Build schedules and run payroll from the same system your team already uses.
• Split tips fairly without doing math on napkins after closing.
• Pay employees different rates for different jobs without separate tracking.
• Know your team clocked in on time with GPS and photo verification.
• File federal, state, and local taxes without becoming a tax expert.

Choose Homebase if: You're done paying for three different systems that don't talk to each other 

Done with separate systems? Try Homebase free and see why 100,000+ small businesses handle scheduling, time tracking, and payroll in one place.

Skip it if: Your entire team is salaried and nobody tracks hours or shifts.

Gusto: Best payroll software for growing businesses

Starting price: $49/month + $6/employee

Best for: Businesses scaling past 15 employees who need HR features alongside automated payroll solutions.

What it does: Gusto runs your payroll processing software and handles the HR work you don't have time for. Health insurance, 401(k) setup, benefits administration—all the stuff that makes you feel like a "real" company without hiring an HR person. New hires complete their paperwork digitally before day one.

What you get:

• Run payroll as often as needed without counting how many times you process.
• Offer health insurance and retirement plans without HR expertise.
• Handle employees in multiple states without researching tax rules yourself.
• Let new hires complete onboarding paperwork from home before starting.
• Track PTO balances automatically instead of maintaining spreadsheets.
• Get alerts when labor laws change so you're not caught off guard.

Choose Gusto if: You're growing fast and need professional benefits without hiring a full-time HR director.

Skip it if: You've got 5 employees and full HR tools feel like using a forklift to move a box.

QuickBooks Payroll: Best payroll software for accounting integration

Starting price: $30/month + $5/employee (Core plan)

Best for: Businesses already using QuickBooks for accounting who want everything connected.

What it does: QuickBooks Payroll lives inside QuickBooks, so your payroll programs and accounting talk to each other without you playing middleman. Run payroll, and your books update automatically. Tax time becomes less painful when everything's already organized in one place.

What you get:

• Stop entering the same data twice into separate systems.
• Get money to employees the same day you run payroll if needed.
• Let the system calculate and file payroll taxes automatically.
• Pay contractors and generate 1099s without separate tracking.
• Add workers' comp administration as you grow into higher plans.
• Avoid tax penalties with Elite plan protection that covers mistakes.

Choose QuickBooks if: Your accountant lives in QuickBooks and you're tired of exporting and importing files.

Skip it if: You don't use QuickBooks and don't want to—the main benefit disappears.

Square Payroll: Best payroll software for budget-conscious retailers

Starting price: $35/month + $6/employee

Best for: Small retail or restaurant businesses using Square POS who need affordable payroll processing.

What it does: Square Payroll connects with your Square register to track sales and labor costs together. See exactly how much you're spending on labor versus making in revenue. Tips get reported and distributed automatically without manual calculations at end of shift.

What you get:

• See labor costs alongside sales data from your POS in real time.
• Handle tipped employees without manual tip reporting headaches.
• Calculate commissions and bonuses based on actual sales performance.
• Get money to employees by next business day, not three days later.
• Pay contractors with automatic 1099 generation at year-end.
• Run payroll from your phone between helping customers on the floor.

Choose Square if: Square already runs your register, and $35 monthly beats paying separately for payroll.

Skip it if: You don't use Square for anything—the integration advantage doesn't help you.

ADP RUN: Best payroll software for scalability

Starting price: Custom pricing

Best for: Businesses planning growth from 25 to 100+ employees without switching providers later.

What it does: ADP RUN handles complex payroll system software that breaks simpler tools. Multiple states with different tax rates? Industry-specific compliance rules? Detailed reporting for investors? ADP assigns you an actual person to call when things get complicated.

What you get:

• Process payroll across multiple states without tracking different tax rules yourself.
• Call a dedicated payroll specialist when you're confused, not ticket systems.
• Stay compliant with industry-specific regulations without hiring a compliance officer.
• Generate detailed reports that satisfy investors or loan requirements.
• Connect time tracking systems as your team grows beyond manual entry.
• Add workers' comp and benefits administration without switching platforms.

Choose ADP if: You're planning serious growth and can't afford to switch systems at 50 employees.

Skip it if: You've got 8 employees and custom pricing costs more than your current needs justify.

Rippling: Best payroll software for automation

Starting price: Custom pricing

Best for: Tech-savvy businesses wanting maximum automation across payroll, HR, and IT systems.

What it does: Hire someone, and Rippling sets up their payroll, benefits, email, computer access, and software licenses simultaneously. Fire someone, and everything shuts off at once. Works for international teams too.

What you get:

• Connect over 600 business apps so data flows everywhere automatically.
• Onboard new hires across payroll, benefits, and IT without repeating information.
• Pay international contractors and employees in their local currencies.
• Provision laptops and software access when someone starts, not three days later.
• Manage health insurance with multiple carrier options in one dashboard.
• Build custom workflows that trigger actions across your entire tech stack.

Choose Rippling if: You want every system connected and automated without lifting a finger.

Skip it if: You run a simple local business where automation feels more complicated than helpful.

Top 4 payroll software benefits for small business

Professional payroll software solves problems that cost you time, money, and sleep. Here's what changes when you stop doing payroll manually.

1. You stop spending Sunday nights calculating hours.

Automated payroll solutions convert timesheets to paychecks without manual math. No more dividing minutes by 60 or second-guessing overtime calculations at midnight.

The best payroll app runs the numbers instantly and catches errors before they become problems. You get your weekends back.

2. You avoid expensive tax penalties.

Tax compliance isn't optional, but it's complicated. Top payroll software calculates federal, state, and local taxes automatically, files everything on time, and keeps you updated when rates change.

One missed deadline costs more than years of payroll software subscriptions.

3. You protect employee data from breaches.

Sensitive information stored in filing cabinets or spreadsheets creates liability. Professional payroll software encrypts Social Security numbers, bank details, and wage data with security measures small businesses can't build themselves.

Your team's personal information stays protected without you becoming a security expert.

4. You eliminate constant paycheck questions.

Employee self-service portals let your team check pay stubs, update tax withholdings, and download W-2s themselves. They stop asking "when do I get paid?" because the best payroll app sends automatic notifications when money hits their accounts.

You answer fewer questions, and they get instant answers.

Best payroll software by business type

The right payroll system software depends on your business size, industry, and how your team actually works.

Best payroll software for small, medium, and large business

Small businesses (1-10 employees):

Homebase and Square Payroll work best for micro-businesses watching every dollar. At this size, you need affordable pricing without sacrificing core features.

Homebase combines scheduling and payroll for hourly teams. Square makes sense if you already use their POS system.

Medium businesses (11-50 employees):

Gusto, Homebase, and OnPay handle growing teams that need more than basic payroll processing software. You're adding benefits, managing PTO policies, and dealing with higher turnover.

These common payroll systems scale with you without requiring a complete switch later.

Large businesses (50+ employees):

ADP RUN, Paychex, and Rippling handle complexity that breaks simpler tools. Multi-state compliance, detailed reporting for investors, dedicated support—these platforms justify custom pricing when you're managing serious headcount.

Best payroll software for specific industries

Restaurants and retail:

Homebase and Square Payroll handle tipped employees without extra headaches. POS integration means labor costs appear alongside sales data.

Tip pooling, reporting, and distribution happen automatically instead of closing-time calculations on bar napkins.

Healthcare practices:

Healthcare businesses need payroll that understands their world. Gusto and ADP handle multiple pay rates for different roles, overtime tracking for shift workers, and proper record retention.

HIPAA compliance comes built-in so you're not researching regulations yourself.

Professional services:

Time tracking integration matters when billing clients. Homebase combines time tracking with payroll for service businesses.

QuickBooks Payroll connects billable hours to accounting for firms already using QuickBooks.

Online payroll software for accountants

Accountants managing multiple clients need different tools than single-business owners.

QuickBooks Payroll leads for accountants already working in QuickBooks. Client switching, consolidated reporting, and direct access to multiple company files save hours monthly.

ADP offers multi-client dashboards with dedicated accountant support for larger practices.

Growing beyond 10 employees? You need payroll that scales without forcing you to start over.

How to choose the best payroll software for your business

Choosing payroll management software that actually works means understanding what you need before comparing features.

Assess your payroll software needs

Team size and composition matter most.

Five hourly employees need different tools than twenty salaried workers. Know your exact headcount and employment types before shopping.

Payment frequency affects your choice.

Weekly payroll costs more with providers who charge per run. Figure out how often you'll process payroll before comparing pricing.

Industry requirements eliminate half your options.

Restaurants need tip management. Healthcare requires HIPAA compliance. Construction wants certified payroll reporting. Start with your industry's specific needs.

Understanding payroll software pricing models

Per-employee pricing adds up fast.

Most payroll software pricing works like this: $40 base + $6 per employee monthly. Ten employees costs $100 monthly. Twenty employees? $160 monthly.

That $6 per person becomes $720 yearly per employee. Do the math before you commit.

Tiered pricing hides real costs.

Basic plans lack features you'll need. Mid-tier plans cost 50% more but include what should be standard.

Calculate the tier you'll actually need, not the advertised starting price.

Watch for extra charges.

Same-day direct deposit, tax penalty protection, multi-state payroll, contractor payments, and year-end forms often cost extra. These "add-ons" can double your monthly bill.

Trial payroll software before committing.

Free trials reveal problems sales demos hid. Run actual payroll with real employee data during trials.

Essential payroll software integrations

Accounting integration prevents double-entry disasters.

Manually transferring payroll data wastes hours and creates errors. QuickBooks users need QuickBooks Payroll. Everyone else needs reliable export options.

Time tracking integration eliminates manual timesheets.

Integrated systems flow hours straight to paychecks. Homebase combines time tracking and payroll so hours convert automatically.

POS integration connects labor to revenue.

Restaurant and retail owners need labor costs alongside sales data in real time. Disconnected systems force manual calculations.

HR platform integration reduces redundant entry.

This matters more as you grow past fifteen employees when administrative work multiplies.

Evaluate payroll software customer support

Support channels determine speed.

Phone support beats email when payroll is due tomorrow. Check what's included—premium support shouldn't cost extra.

Implementation help makes switching your new payroll system easier.

Some providers assign specialists who configure everything. Others email PDFs and wish you luck.

Ask specifically what setup support includes before you start.

Self-service resources matter at midnight.

Good help documentation answers common questions before payroll deadline. Test their knowledge base during trials.

If you can't find answers easily, neither will your team.

Stop comparing features. Start a free trial and run real payroll to see what actually works.

Types of payroll systems: Cloud vs. on-premise

Most small businesses choose cloud payroll software today. Here's why that shift happened and when on-premise still makes sense.

Cloud payroll software advantages

Access from anywhere.

Run payroll from your phone. Check labor costs from home.

Web based payroll software works wherever you have internet.

Automatic compliance updates.

Tax rates and labor laws update automatically. On-premise software requires manual updates you'll forget.

Built-in security.

Hosted payroll software encrypts data, backs up automatically, and meets security standards small businesses can't build themselves.

Lower costs.

Cloud payroll starts at $30-50 monthly. On-premise systems cost hundreds upfront plus annual maintenance.

Best providers: Homebase, Gusto, QuickBooks Payroll, and Square Payroll lead for small businesses.

On-premise payroll software considerations

Rarely worth it for small businesses.

Large enterprises with IT departments sometimes choose on-premise systems. You need servers, IT staff, and backup systems.

Small businesses almost never benefit from this complexity.

Trade-offs you're accepting.

Manual compliance updates. No mobile access. Higher upfront costs. Ongoing IT maintenance.

In-house payroll software or inhouse payroll software requires resources most small businesses don't have.

Integrated HR and payroll software

Combined systems eliminate redundant work.

The best hr and payroll software connects hiring, onboarding, benefits, time tracking, and payroll. Enter information once, use everywhere.

Worth it at scale.

Small teams under ten might not need full integration. Growing businesses past fifteen employees save hours weekly with integrated payroll processing systems.

The ROI appears when administrative work multiplies.

Why Homebase is best payroll software for hourly teams

Most payroll software treats hourly teams like an afterthought. Homebase built everything specifically for how hourly businesses actually work.

Scheduling, time tracking, and payroll work together instead of forcing you to manage three separate systems. Hours flow automatically from time clock to paycheck without spreadsheets or manual entry.

Tips get tracked and distributed correctly. Multiple pay rates per employee work without complicated workarounds. PTO accrues automatically based on hours worked.

Join 100,000+ small businesses using Homebase. Start your free trial and see why hourly teams choose us for scheduling, time tracking, and payroll.

{{banner-cta}}

‍

Best payroll software: Frequently asked questions

What is the best payroll software for small businesses?

It depends on your team structure. Homebase works best for hourly teams needing scheduling and time tracking together. Gusto fits growing businesses adding HR features. QuickBooks Payroll makes sense if you already use QuickBooks. Choose based on how you actually work, not just the lowest price tag.

How much does payroll software cost?

Expect $30-50 monthly base plus $4-8 per employee. Homebase charges $39 + $6 per employee monthly. Ten employees runs around $100 monthly total. Watch for sneaky extras—same-day deposit fees, tax penalty protection, multi-state processing—that can double your actual bill.

Does payroll software handle taxes automatically?

Yes, it calculates and files your taxes without you becoming a tax expert. This includes quarterly 941 forms, annual W-2s and 1099s, and state unemployment taxes. Automatic tax filing is why most small businesses finally ditch manual payroll after their first penalty scare.

What is the most popular payroll software?

Gusto, QuickBooks Payroll, ADP, and Homebase lead for small businesses. Gusto wins with businesses prioritizing HR features. QuickBooks dominates among accounting-focused owners. Homebase leads for hourly teams who need scheduling, time tracking, and payroll working together instead of separately.

What payroll software integrations matter most?

Accounting, time tracking, POS, and HR integrations save the most time. Accounting integration prevents double-entry disasters. Time tracking integration eliminates manual timesheet copying. POS integration shows labor costs against revenue in real time. QuickBooks users need QuickBooks Payroll. Hourly teams need time tracking integration like Homebase provides.

Can I run payroll manually?

You can, but you probably shouldn't. Manual payroll means you're calculating taxes, filing on deadline, and maintaining records yourself. One missed tax deadline costs more than years of software subscriptions. Most businesses switch after their first penalty or when they realize Sunday nights aren't for payroll math.