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6 Min. Read

Top 5 Best Online Payroll Software for Small Businesses

Top 5 Best Online Payroll Software for Small Businesses

Let’s take a look at the best online payroll software on the market for small businesses. 

As a small business owner, you know that managing payroll can be time-consuming. 

The alternative is to outsource which can be expensive. 

So, what’s the middle ground? 

Online payroll software. 

It can be the answer to automating aspects of your payroll process. It’s a relatively cheap service that can make your life a little easier. 

There are now many payroll provider options that have developed specialist online software. Here are a few of the best options available. 

Here’s What We’ll Cover:

What Is the Purpose of Payroll Software?

What Are the Benefits of Online Payroll Software?

5 of the Best Online Payroll Providers 

Key Takeaways

What Is the Purpose of Payroll Software?

To help small business owners automate their payroll processes. 

It also saves time and effort while minimizing the risk of human error. 

Online payroll software also helps small businesses to keep the payroll process in-house. 

If you’re looking for some help in finding a payroll provider to suit you, you’ll find some tips here

What Are the Benefits of Online Payroll Software?

  1. It saves time. Automating the payroll process saves time on otherwise tedious manual tasks. It also usually includes facilities for time-tracking and filing of payroll taxes. 
  2. Costs saved on labor. An online payroll service saves on the labor costs of processing payroll. 
  3. Accurate payroll processing. Automating the process mitigates the risk of human error. It also alerts you to deadlines so you can avoid the risk of payroll tax penalties for forgetting to file. 
  4. Integrate with your accounting software. You need to be able to see your business’s finances all in one place and software providers know this. This is why many providers will integrate payroll with your accounting software

5 of the Best Online Payroll Providers 


Gusto is a simple and modern payroll solution designed for small business owners. 

It allows you to run payroll in minutes. 

It also takes care of calculating, filing, and paying your payroll taxes. 

Gusto brings together your HR, employee benefits, and payroll all in one place. 

The integration with FreshBooks syncs your payroll expenses to your FreshBooks account. This way you always have a clear picture of your business’ finances.

Best Features of Gusto 

  • It’s cloud-based so you can use it from anywhere 
  • Clear, easy, and reasonable pricing structure. Price includes setup, customer support, and integrated compliance features 
  • Run unlimited payrolls for every state and file W-2s and 1099s without any extra cost 
  • Employees get their own accounts. They can use it to choose the benefits they want such as health insurance and view their paid-time-off entitlement
  • No extra charge for workers’ compensation, wage garnishment, and time-tracking integration 

QuickBooks Payroll 

QuickBooks Online Payroll is an obvious choice if you already use QuickBooks Online for your accounting. 

The cloud-based online payroll service is designed with small businesses in mind. It automates your payroll while offering next or same-day direct deposit.

Best Features of QuickBooks Payroll 

  • User-friendly system 
  • Make direct deposit payments either the same day or the next day 
  • Tax filing comes as standard with each payment tier. This includes automatic calculation, filing, and payment of federal and state payroll taxes
  • Excellent employee services. They can access pay stubs, W-2s, and paid-time-off balances through their account 
  • Automatic payroll for salaried employees 
  • Integrates with QuickBooks Online
  • Comes with an accuracy guarantee. If something goes wrong that’s not your fault, QuickBooks will pay any tax penalties 


OnPay offers a payroll software service designed for small businesses. It can also cater to some larger companies and also those in specialized areas. 

More than just payroll, OnPay can handle your Human Resources and employee benefits. 

Best Features of OnPay 

  • Affordable monthly cost. The cost includes unlimited pay runs, quarterly and year-end tax filings, and HR tools 
  • Handles all state and federal tax payments 
  • Accounting and time-tracking integrations 
  • HR features like employee onboarding process, tracking time-off requests, and access to a team of benefits brokers
  • Free payroll setup 

Patriot Payroll

Patriot Payroll is known for being easy to use. Its payroll software for small businesses is easy to set up. There is also a clear pricing structure that some other services are lacking. 

Patriot Payroll prides itself on helping small business owners do their payroll in only a few minutes. 

Best features of Patriot Payroll 

  • The cost of the service is low compared to others. Choose between full-service payroll and basic payroll options. This makes it more affordable for small businesses. Cost is also advertised in a transparent and accessible way 
  • The software supports up to 100 employees which is more than others at the same cost 
  • Plenty of helpful resources to help you get started on the system
  • Pay independent contractors and employees on the same payroll 


Another cloud-based payroll and human resources software available is Paychex. 

It assists small businesses who need some help with these services but don’t want to fully outsource.

Best Features of Paychex 

  • Every plan comes with some interesting features. You can find New-hire state reporting, automatic payroll tax filing, and an employee financial wellness program. 
  • Paychex offers over 160 reports with its payroll and HR packages 
  • Free mobile app for business owners and employees 
  • The option for payment by direct deposit, paycards, and paper check
  • Pay hourly employees as well as salaried and contract 

Key Takeaways

Payroll experts have worked to create online payroll software solutions for businesses. 

Small businesses have enough on their plate as it is. 

Automating your payroll process frees up a little more time in your day. It also makes sure your employees get paid on time and in the right amounts. Choosing a system that incorporates the filing of payroll taxes keeps you compliant without the hassle. 

Choosing payroll software that integrates with your accounting will also help you to keep on top of your business’s finances. 

How to Set Up Payroll for a U.S. Business