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.

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.

  • No hidden fees
  • Easy to use
  • Good value for the cost
  • Affordable for small businesses
  • Pay employees anywhere in the world
  • Integrate with more than 500 apps
  • No same-day or next-day direct deposit
  • No automatic payroll submission


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.

  • Easy to use and learn
  • Integrates well with other systems and flexible with 3rd party applications
  • Provides good accounting reports
  • Affordable price
  • Easy to access from any device – phone, tablet and computer (depending on the version)
  • Easy to find and fix errors/mistakes
  • Easy to look-up customer information
  • Lack of industry and business-specific features (such as lot tracking, eCommerce and barcode scanning)
  • Lack of key reports outside of accounting
  • Built with a “small business mindset”
  • Lacks invoice design tools


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.

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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.

  • Easy invoice entry – with a few clicks you can enter an invoice for payment and then find it when it’s time to pay.
  • Easy reporting – finding financial reports is quick, easy, and accurate!
  • Printing checks is simple – you can do a batch payment in a matter of minutes.
  • Only checks can be received into Sage – credit card payments cannot be taken.
  • Entering a credit from a vendor or customer can be cumbersome.


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.


4.  ADP Payroll Software

One of the most well-known names in payroll and HR is ADP. The brand recognition and years of experience make it ideal for large companies or businesses that plan on growing pretty fast. The lowest-priced plan includes full-service payroll, direct deposit, reporting, and a self-service employee portal. More complete features and HR services come with higher-priced plans.

  • Scalable with several plan options
  • Robust reporting, including customization
  • Lots of HR add-ons
  • Pricing isn’t transparent
  • Possibly too many features for small businesses
  • Several fees, including for setup


Key Features Of ADP Payroll

  • Payroll system ideal for one to 49 employees
  • Payroll processing
  • Direct deposit
  • Debit card payment available
  • Tax filing
  • General ledger interface
  • New hire reporting
  • ADP employee access
  • HR tips w/newsletter
  • HR checkups
  • Electronic reporting
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Consider ADP’s main competitors and you’ll see why it’s typically used by larger businesses. ADP has always been more of a professional employer organization (PEO), but it has evolved to offer a payroll service that’s more suitable for small businesses. It’s a good idea to choose a payroll service that can grow with your business, though, if only so you can avoid migrating data to a different service in the future. ADP makes that possible with its ADP RUN service, which is best for businesses with fewer than 50 employees. 

Unfortunately, it isn’t easy to compare the cost of ADP’s plans to other services because ADP doesn’t publish its plans’ pricing. You’ll have to fill out forms to get a custom quote for your business, which will be based on your needs and the number of employees your business has. We received a variety of quotes and setup fees for a 10-person business, which fell between $150 to $200 per month, making it an expensive choice compared to all the software on this list. Setup fees ranged from $25 to $200, but reps often offered to waive the fee if we signed up immediately.


5. Paychex Payroll Software

Paychex Flex offers more than 160 reports for you to get a clear look at wages, taxes, turnover, and more. Paychex is our best reporting option because it checks almost all the boxes for what you’d want in payroll software when it comes to reports and data. It also automatically files your payroll taxes, gives you unlimited payroll runs, ensures compliance, and includes integrations with important programs you also use, such as accounting and benefits apps.

  • 24/7 support
  • Easy to use
  • HR add-on options
  • Robust reporting feature
  • Even the lowest-priced plan is pricey
  • Hidden fees for setup & EOY tax docs
  • Mixed reviews from users regarding support


Key Features Of Paychex:

  • Payroll and taxes
  • Small and large business payroll
  • Taxation
  • Online payroll management
  • HR services
  • Analytics and reporting
  • PEO
  • COBRA administration
  • Employee screening
  • Background checks
  • Applicant tracking
  • Online hiring
  • Employee benefit and insurance services
  • Retirement plan management
  • Payment processing
  • Expense management

There’s a lot to like about Paychex. The payroll software makes it easy to set up and run payroll, it automates submission of federal, state, and local payroll taxes, and it offers plenty of upgrade options, which you may need as your business grows. Still, the basic reporting you get from Paychex could be worth the monthly fee alone, giving it the edge in this category. Plus, you’ll be able to add any other data field you’d like, thanks to custom fields, which is rare for small business online payroll services.

It’s difficult to say how much Paychex will cost you unless you go through the process of getting a custom quote. The lowest-priced plan starts at $59 per month, plus $4 per person per month, which is more expensive than most other small business payroll solutions (and you don’t get all those sweet reports at this tier). 

One of the most important aspects of a good online payroll solution is whether it integrates with software you already use. Paychex does integrate with QuickBooks and Xero accounting software, plus many health insurance and benefits apps, time tracking and attendance software, and HR software.


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.

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