Best Online Payroll Services for Small Businesses in 2025

As your small business grows, DIY payroll eventually loses its charm. Dreaded spreadsheet mistakes and juggling tax deadlines are a surefire way to get overwhelmed. The good news? Online payroll services can help you out!

These platforms save time, reduce errors, and help keep you compliant—so you can spend less time crunching numbers and more time growing your business. Let’s explore the pros and cons of different services so you can find the perfect match for your growing team.

TL;DR: Our top picks for payroll processing software

Here’s a quick and simple overview of the best online payroll services for small businesses as of 2025:

• Homebase - Best for growing small businesses with hourly employees. We provide over 100k small businesses with payroll, scheduling, HR, hiring and more—all in one free mobile app! Check out the Homebase Payroll Guide for a deeper look.
• Gusto - Best for prioritizing all-in-one payroll and HR platform, but wouldn’t mind paying extra for time & attendance tools.
• QuickBooks - Best for businesses already using QuickBooks for accounting.
• ADP RUN - Best for compliance backup for businesses with under 50 employees.
• Square Payroll - Best for Square POS customers, such as small retail or restaurant businesses.
• OnPay - Best for small businesses that do not want automated payroll but are still looking for full-service options.
• Patriot Software - Best for budget-conscious small businesses that don’t need help with tax filing.
• Paychex Flex - Best for hands-on help from dedicated specialists.
• SurePayroll - Best for households paying for nannies and domestic care, as well as very small businesses and freelancers.
• Zenefits - Best for businesses that want strong HR tools with payroll as a paid add-on. 
• Rippling - Best for teams that want HR, payroll, and IT in one place and can take a pick-and-choose approach.
• Wave Payroll - Best for Canadian or U.S. freelancers already using Wave’s free accounting tools.

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{{banner-cta}}What are online payroll services and how do they work?

Online payroll services are cloud-based tools that help small businesses handle payroll without manual work.

While each online payroll provider has its own perks and quirks, the most common features include:

• Employee payments through direct deposit
• Federal, state, and local tax filing
• W-2s and 1099s
• Time tracking and PTO
• Compliance support

You can handle payroll in-house with a bookkeeper or HR person—or do it yourself, if you’re feeling confident. But this route leaves more room for mistakes, and it gets harder to manage as your team grows. Hiring an accountant adds expertise, but it can be pricey for a small or growing business.

Online payroll services are super accessible if you’re new to setting up payroll, and can grow with your business. Plus, some services also come with employee portals, so your staff can clock in and have all of their employment paperwork in one place.

Key features to look for in the best online payroll services

Here are the must-have features of online payroll services that save you time and tax headaches:

• Automatic tax calculations and filing: A good payroll service handles tax calculations, filings, and year-end forms like W-2s and 1099s. This keeps things accurate and compliant, without the manual work.
• Employee self-service portal: Employees should be able to access their pay stubs, tax forms, and update their info on their own. Keep an eye out for small company payroll services that also include apps (Psst—we do that).
• Direct deposit and contractor support: Look for flexible pay options like direct deposit and tools to pay contractors, too. Independent contractor laws work differently than employee laws, so it’s helpful to have features that keep that in mind.
• Benefits management: Some platforms help you offer health insurance, retirement plans, and other perks. Others integrate with benefits providers so deductions show up in payroll without extra steps.
• Integration with accounting software: Connecting payroll to your accounting tools means less manual entry and cleaner books. It’s a major time-saver for bookkeeping.
• Support for compliance and multi-state payroll: If you’ve got team members in more than one state, your payroll system should handle different tax rates and labor laws. Automatic updates help keep you compliant as rules change.
• Transparent pricing with no hidden fees: Pricing should be clear and upfront. Watch for extras like charges for direct deposit, tax forms, or contractor payments—some services include them, others don’t.

12 Best online payroll services for small businesses (2025)

So let’s get into it—here are small business payroll software options and their specialties!

1. Homebase

Homebase is best for hourly teams that want to make scheduling a breeze. On top of tools like scheduling, timesheet, and POS integration, we also offer online payroll services! We automatically calculate hours, breaks (with reminders!), overtime, PTO, and wages so you can focus on the fun parts of growing your business.

Key features:

• Automatic payroll that you can run as often as you need at scheduled times.
• Compliance features that keep you up-to-date with PTO policies, taxes, labor laws, and FLSA rules.
• Tax calculation and filing for federal, local, and state taxes.
• Employee perks like payday notifications, tip distribution, and quick access to schedules and hour-tracking.
• All-in-one mobile app for scheduling, hour tracking, and payroll.
• Automatic calculation: Hours, breaks, overtime, PTO, wages—we got it all in one place.

Pricing: $39/month base fee + $6/month per employee paid

Free trial: No trial, but employee scheduling is free for teams of 10 or less

Looking for a new payroll provider? We can help you make the switch! Seriously, in under 30 minutes we can knock through data transfer with zero setup fees and onboarding support from a payroll expert.

Get in touch so we can get your payroll all set up!

2. Gusto

Gusto is best for small teams that want an easy, all-in-one payroll and HR platform. It’s user-friendly, automates busywork, and scales well as you grow. However, time & attendance tools are only included in higher plans.

Key Features:

• Automated payroll & tax filing
• Employee self-service portal
• Health benefits and 401(k) support
• Contractor-only packages available

Pricing: Starts at $49/month base + $6/employee
Free Trial: Not listed.

3. QuickBooks Payroll

QuickBooks Payroll is the best online payroll provider for businesses already using QuickBooks for accounting. It syncs your books and payroll effortlessly, but requires higher tiers for hour-tracking.

Key Features:

• Auto payroll for employees who work consistent hours
• Worker’s compensation packages
• Tax form filing
• Free guided setup

Pricing: Starts at $25/mo + $4/employee
Free Trial: Not listed

4. ADP RUN

ADP RUN is best for small businesses that expect to grow or need compliance backup. It offers enterprise-grade tools with full support, and has a package specifically for companies with under 50 employees.

Key Features:

• Multi-state and local payroll & tax filing
• 24/7 customer support
• Mobile app for employees
• Easy integration with time-tracking and HR

Pricing: Contact for a custom quote

Free Trial: Not listed

5. Square Payroll

Square Payroll is the best online payroll provider for small businesses already using Square POS or managing hourly staff. It’s a great online payroll provider for retail or restaurant teams.

Key Features:

• Full-service employee and contractor payroll options
• Unlimited monthly pay runs
• Pay by check, direct deposit, or Cash App
• Direct-tip tracking and importing

Pricing: $35/month + $6/employee; $6/contractor-only plan
Free Trial: Not listed

6. OnPay

OnPay is best for small businesses wanting flat-rate, full-service payroll and HR. You get a ton of tools without any surprise add-on fees, but it doesn’t have automated payroll—meaning you have to manually run things each month.

Key Features:

• Free data migration if you’re switching payroll providers
• Unlimited payroll and tax filing in all 50 states
• Robust HR resources
• Compliance audits

Pricing: $49/month + $6/employee

Free Trial: 30-day free trial available

7. Patriot Software

Patriot Software is best for budget-conscious small businesses that need basics done well. Note that it’s pretty no-frills—the basic plan doesn’t have tax filing options, and HR and time tracking require separate add-ons.

Key Features:

• Free contractor and employee portals
• Up to five different pay rates
• Mobile friendly for people who don’t like apps
• Unlimited back-end users

Pricing: Starts at $17/month + $4/employee
Free Trial: 30-day free trial, and 50% off for 3 months

8. Paychex Flex

Paychex Flex is best for growing businesses that want hands-on help and scalable payroll tools. When it comes to payroll for small business growth, the basic plan is pretty limited, so pricing can climb depending on the features your business currently needs.

Key Features:

• Dedicated payroll specialists
• Automatic tax administration (Taxpay™)
• Multiple pay options for employees
• Employee app with financial management tools

Pricing: Contact for a custom quote
Free Trial: Not listed

9. SurePayroll

SurePayroll is best for very small businesses, freelancers, or households paying for nannies. Because of its niche, it costs extra for timeclock, accounting, or HR tools.

Key Features:

• Automatic payroll
• Free 2-day direct deposit
• Live phone and chat support
• All taxes calculated (and deposited with Full Service!)

Pricing: 

• No Tax Filing: $20/month + $4/employee
• Full Service: $29/month + $7/employee

Free Trial: 6-month free trial available

10. TriNet (previously Zenefits)

Zenefits is best for businesses that want strong HR tools with payroll as a paid add-on. It’s perfect if employee benefits and compliance are your top priorities—but if payroll is your number one need, you might want to explore more options.

Key Features:

• Support from HR professionals
• Comprehensive healthcare benefits
• Benefits administration
• Compliance tools and support

Pricing: Contact for a demo and quote

Free Trial: Not listed

11. Rippling

Rippling is best for tech-savvy or fast-growing teams wanting HR, payroll, and IT in one place. It has lots of different solutions for you to pick and choose from, so you can assemble your perfect package, but pricing will depend on add-ons.

Key Features:

• Global payroll support
• Time off and PTO tracking
• Job codes and multiple pay rates
• Federal, provincial, and local taxes for Canadian clients

Pricing: Modular pricing, contact for a quote and demo

Free Trial: None listed

12. Wave Payroll

Wave Payroll is best for Canadian small businesses (except for in Quebec) or U.S. freelancers already using Wave’s free accounting tools. For Wave customers, this online payroll provider convenient to manage tax filing

Key Features:

• Data-migration if you’re switching platforms
• Integrates with Wave accounting
• Full-service Canadian and US tax support
• Tools for employees and independent contractors

Pricing: 

• $40 USD + $6 per active employee
• $25 CAD base fee + $6 per active employee

Free Trial: Not listed

How to choose the right payroll provider for your small business

With all those solid online payroll companies in mind, all that’s left is to choose the one that hits your unique needs.

Here are some key questions to ask:

• What size is your team? A team of 1-5 has different needs than a team of 50. Many online payroll companies have per-employee charges, which can make a difference in your monthly fees if you’re experiencing rapid growth. 
• Are you managing independent contractors and W-2 employees? Misclassifying independent contractors and employees is a pretty common compliance mistake. Separate tools for each type of employee can get your bases covered.
• Do you need benefits and HR tools too? Let’s be real: don’t pay for stuff you don’t need. If you’re budget-conscious, start with your most basic needs. Plenty of online payroll services have the option to upgrade or add on more tools later!
• Do you process payroll across multiple states or provinces? Tax requirements look different on a state and local level. You’ll save yourself a whole lot of time if your online payroll provider factors those state-level laws and taxes.
• How important is customer support? If you’re truly a payroll newbie (or feel intimidated by new tech), customer support saves you extra money on an accountant to manage your questions.

Ultimately, there are three key things to keep in mind: cost, functionality, and scalability. The best online payroll services should hit all three, but if you’re still uncertain about which one to choose, rank how important each factor is to you and go from there.

Is there a free or cheap payroll service?

To be honest, free payroll processing software isn’t really a thing. Don’t get disheartened though—if you’re not running a huge company, there definitely are some cheap payroll services for small businesses.

Here are some options to consider if you’re doing small business payroll on tight budget:

• Homebase Payroll: Our Basic plan covers scheduling, time tracking, and POS integration for up to ten team members a month for free. The payroll add on is $39/month + $6/employee, but if our base features are your priority, the savings really shake out!
• Square Payroll: Same deal—for Square customers, pricing comes out at $35/month + $6/employee. However, if you’re hiring contractors only, payroll features are $6/month flat! This might be a great choice if it suits your current setup as a Square customer.
• Patriot: With the Basic plan at $17/month + $4/employee, Patriot is the cheapest online payroll service you’ll find. The catch is that it doesn’t come with any tax filing options, which is one reason most people start looking into online payroll services for small businesses.

Can I do payroll online myself?

The spreadsheet method has been used by small business owners for years, and there’s nothing stopping you from sticking to it. But going DIY does come with the risk of manual errors that can lead to compliance issues or (ugh) IRS penalties.

If you’ve got an accounting background and the time to handle the paperwork yourself, feel free to take a crack at payroll. But if you feel lost about the basics of how payroll works and don’t have the budget to hire an accountant, online payroll companies have you covered.

FAQs About Payroll Services for Small Businesses

Got questions about payroll for small businesses? Here’s a quick guide to the essentials before diving in:

What’s the best payroll for a small business?

There’s no one-size-fits-all answer—your best option depends on your team size, budget, and whether you need extra features like benefits management or scheduling. 

For example, if it’s your first time managing an hourly team with big scheduling needs, Homebase is a good bet. But if you’re already a Square or QuickBooks customer (and you’re happy that way), their payroll services might work for you. 

How much do online payroll services cost?

Most platforms charge a base monthly fee (often $30–$50) plus a per-employee fee ($4–$12). Some services offer contractor-only plans at lower rates, and a few even have free versions with limited features. Just keep an eye out for extras like year-end tax form fees or add-ons.

Can payroll software handle taxes and compliance?

The best online payroll services absolutely handle taxes and compliance! This includes automatically calculating, filing, and paying your federal, state, and local payroll taxes. Many also help you stay compliant with labor laws—especially if you operate in multiple states or have hourly workers with overtime.

What documents do I need to get started?

To run payroll, you’ll typically need your Employer Identification Number (EIN), employee or contractor details (like W-4s or W-9s), your bank account info for payments, and any state or local tax IDs. Ideally, your online payroll provider should walk you through these steps.

Do I need payroll software if I only hire contractors?

Not always—but it can still be worth it. Contractor-only payroll plans are often affordable, and they’ll help you track payments, send 1099s, and stay on top of tax rules. It’s a great way to stay organized as you grow.

The right payroll provider makes all the difference

Running a small business is a big job—payroll should make it easier, not harder!

The best online payroll services should keep things simple, save you time, and grow right along with you. With manual payroll off your plate, you can put the energy into doing what you love: focusing on growing your business.

Itching to get started? Hit us up to see if Homebase is the right option for you!

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