5 Best Payroll Software For Small Business

If you are searching for the best payroll software for small business, this article will guide you in the right direction by helping you save time, money and effort in the long run.

Being a responsible small business owner, you must pay your employees accurately and in a timely manner. You should also file and remit payroll taxes accurately to the IRS without any delay.

Having in-house payroll software will help you administer payroll with total control, and saves you time, money, and costly mistakes.

Before we start, you should understand that payroll is one of the most important components of your business.

Whether you’re running your own Scorp or an entire HR department, you need the best payroll software that addresses your unique challenges and enhances the efficiency of your process. in this article, we’ll cover the best payroll software for small business, We’ll go over their features and benefits that will help you determine whether it is suitable for your business or not.

Want to get right to the point? Our top picks for the best payroll service definitely OnPay.

1. Onpay: Best Payroll Software

OnPay offers an easy-to-use, affordable online payroll solution that’s ideal for small businesses. There are no hidden fees, which is important for a small business on a budget. The full-service payroll automates calculations and files your federal, state, and local payroll taxes. You’ll still have to run and approve payroll each time.


Features included with OnPay Payroll services are:

  1. Tax accuracy guarantee
  2. Certified payroll professionals
  3. Free data migration and setup
  4. Unlimited pay runs
  5. Integrated 401(k)
  6. Automated tax payments
  7. No charge for cancellations
  8. Print checks on site
  9. Pay by direct deposit
  10. Pay by debit card
  11. Online employee portal
  12. Employee self-onboarding
  13. Export payroll data
  14. Lifetime accounts for employees
  15. Digital paystubs
  16. Freephone, chat, email support
  17. Integrated health benefits
  18. Integrates with Quickbooks, Xero
  19. Mobile friendly
  20. Pay 1099 contractors
  21. Tax filings for non-profits and clergy
  22. Multiple state payroll
  23. Custom payroll reports

Setting up payroll the first time in a new program can be time-consuming, but OnPay makes it easier with its setup wizard. Follow the steps and make sure your information is accurate, and you should be just fine. If you have data from another payroll service that you want to import into OnPay, you can get help with that, and OnPay guarantees accuracy. 

From “hire to retire,” Paychex offers an incredible number of services, including payroll, HR, benefits administration, business insurance, retirement plans, health care, and more. These features make Paychex a good solution for businesses looking to manage multiple areas of their payroll and HR duties in a single platform.

Onpay is easy to use and offers strong employee management, direct deposit, 100+ reports, two-day payroll processing, and some unique touches, such as an employee handbook builder, a financial wellness program for your employees, and advanced analytics. The more expensive payroll plans also come with built-in HR, onboarding, employee screening, and garnishment services. Plus, Paychex offers 24/7 customer support and takes care of the entire implementation process for you — and it will even calculate and file all of your payroll taxes.

Note: Onpay is our choice as the best online payroll service for larger businesses.


2. QuickBooks Payroll

Another top payroll software option for small businesses is QuickBooks Payroll. If you’re already using QuickBooks accounting software to keep track of your business’s finances—as many business owners are—then this will be one of the easiest ways to automate your payroll. In fact, if you’re using QuickBooks Online, you’ll be able to turn on this payroll software with the click of a button in your accounting software.


QuickBooks Payroll Features:

  • Payroll taxes are done for you
  • Same-day direct deposit
  • Free W-2s filed and sent for you
  • Assistance setting up payroll
  • User-based permissions
  • Premium time tracking (via mobile app)
  • An HR support center
  • Their no-penalty guarantee for tax filing

There are three versions of QuickBooks Payroll software that you’ll be able to choose from. The first plan option for you is QuickBooks Payroll Core, the self-service version of QuickBooks Payroll software. This product allows you to calculate paychecks, pay your employees, and calculate and file year-end forms. For your first three months with this payroll software, you will only have to pay a base cost of $13.50 per month, along with $4 per employee per month. After those first three months, your base cost will increase to $45 per month, but your employee cost will remain the same.

If you want to access more help from your payroll software than the basic version of QuickBooks Payroll can offer you, then consider leveling up to the Premium version. With Premium QuickBooks Payroll, you’ll be able to access all the features that the Self Service version offers, along with the following list of additional features:

For these extra features that Premium QuickBooks Payroll offers, though, you’ll have to pay more—your first three months will come with a discounted base rate of $22.50 a month and subsequent months will come with a base rate of $75. Again, each employee you add to your payroll will cost you $8 per employee per month.

Finally, there is QuickBooks Payroll Elite—the most comprehensive payroll product QuickBooks offers. With this package, you’ll get everything included in the Core and Premium packages, plus the following features:

  • Employee onboarding handled by QuickBooks
  • Time tracking with geofencing
  • Tax penalty-free guarantee
  • Additional customer support for US-based businesses
  • A personal HR advisor

For all of these additional perks, you’ll pay a starting rate of $37.50 for three months. After three months, your rate will increase to $125 per month, plus $10 for every employee you add.


3. Key Features of Sage Payroll

Sage Business Cloud payroll software offers a two-tiered package that's designed to meet the needs of any sized company. The first tier is aimed at SMBs that have ten or fewer employees and therefore don't need complicated bookkeeping services that would better fit large firms.


Key features of Sage Payroll

  • Integration with Sage One Accounting
  • Accounting
  • Daily backup
  • SARS compliant
  • Self-service portal
  • Online payroll management
  • Real-time reporting
  • Secure data storage
  • 256-bit encryption
  • Live dashboard
  • Tax management
  • Multiple format support
  • Remote access to financial records & payslips

Enterprise customers that have many employees can instead opt for the second tier, which can function with large employee enrollment figures not found among smaller firms. This might also be an attractive option for those who compile payroll information for outside companies.

The total cost of either of these two payroll services is dependent on the number of employees paid. Companies that only need to keep track of a handful of employees and maybe a few temporary workers can ultimately save a great deal of money by carefully specifying the exact number of permanent workers and thus taking advantage of discounts.

As well as the usual tax solutions that most payroll software comes with, Sage now allows users to manage ACA compliance as well. It provides suggestions about how to best minimize tax liabilities related to health insurance as well as automatically complies with federal reporting requirements to eliminate the risk of owing money simply because a form wasn't filled out.

Both the Basic and Enterprise-level options come with HR compliance tools and the ability for employees to access W-2 forms. Since Sage Business Cloud combines so many tools into one package, it can easily replace five or six different programs that may be presently in use.


6. Zenefits — The Best For Benefits Administration

As you can probably guess from the name, Zenefits specializes in benefits administration.

Zenefits is actually a full-service HR solution, as opposed to a platform specifically designed for payroll. In fact, payroll doesn’t come standard with any Zenefits plans. But it’s a cheap add-on for just $6 per month per employee. 

For a limited time, you can get one year of free payroll with an annual plan.

Zenefits makes it easy to integrate employee benefits into your HR system. This gives your staff the ability to browse, compare, select benefits on their own from an online self-service portal or mobile app.

You can use your own broker or work with one of the Zenefits broker partners. Benefits include:

  • Health insurance
  • Dental insurance
  • Vision insurance
  • 401(k)
  • FSA and HSA
  • Life and Disability
  • Commuter benefits
  • Supplemental benefits

As I said before, the benefits administration features are the main reason why businesses choose Zenefits over other HR tools. The payroll feature is a nice add-on. 

There are three base price plans for Zenefits:

  • Essentials — $8 per month per employee
  • Growth — $14 per month per employee
  • Zen — $21 per month per employee

Again, payroll is NOT a standard feature in any of these packages. The add-on costs an extra $6 per month per employee. But even as an add-on, it gets the job done. Larger organizations will likely find Zenefits a bit limiting. If you have 100+ employees, this probably isn’t the best option for you. 

Try a free 14-day demo with no credit card required. 


5. FreshBook Best Accountiong Software

FreshBooks started its life as an invoicing solution. Over the years, it has expanded in scope and grown into the go-to online accounting service for sole proprietors and startups. Its popularity extends to small to midsize businesses (SMBs) in many cases. The site went through a major update a few years ago, and many features in FreshBooks “Classic” were left behind, though they continue to be reintroduced. This new FreshBooks is the best choice for the smallest businesses because of its exceptional usability and aesthetic properties—and its smart selection of features. It is our Editors' Choice pick in the freelancer category.


FreshBooks Accounting Software Overview

FreshBooks is one of the biggest names in the invoicing and accounting scene and is the software choice for over 10 million customers. FreshBooks has a number of key accounting features, double-entry accounting, and numerous integrations. FreshBooks has finally stepped up to the plate with its feature-set and joined the big leagues with other accounting competitors, such as QuickBooks Online and Wave.

While there are several positive aspects to this accounting software, there are still several drawbacks to consider. The app is expensive. Each plan only comes with one user, so the cost of additional users adds up fast. There are also some features missing that you’d find with other accounting software, such as built-in payroll.

Despite these drawbacks, FreshBooks is incredibly easy to use and has some of the best customer support on the market. It’s also one of the few programs to offer built-in proposals. This software could be a good option for some small businesses.


The Bottom Line

Now that you’re familiar with the best payroll software for small businesses, it’s time to start deciding which of these four options will be the best fit for your payroll needs and preferences.

Onpay Payroll has been awarded among the Top 10 Payroll Software Companies in the USA by HR Tech Outlook Magazine. Onpay Payroll is the most simple, flexible, and affordable alternative to cloud-based / online payroll software or online payroll services providers.

As a small business our self, we understand the unique payroll needs of small businesses that make us an ideal choice. We consider Onpay Payroll as the best payroll software for small businesses in the market that not only saves the time of small business owners but also saves a considerable amount of money in the long run.

With Paychex, you can manage payroll with ease and accuracy.

How We Chose the Best Payroll Software

We explored 15 different payroll services before choosing the top eight listed here. One of the most important things to consider for any business is cost, which is why that was heavily considered for each option. We made our decisions due to features like direct deposit and reporting. We also sought options with helpful support to help business owners address questions they have with setting up and running payroll.