payroll software small business

Small business owners face various challenges, not necessarily the same magnitude as those of corporates and enterprises, but they’re similar in many ways. In the eyes of the tax collector, however, any and every form of business is liable to submitting and/or filing returns, thus small businesses that don’t do so get penalties in the form of fees or fines, and this includes payroll errors.

However, there’s a lot that goes into working on the payroll system, much time and energy is also spent trying to understand it, but businesses opt to use payroll services instead, so they don’t have to worry about the errors, or legal mistakes, and save time in the process.

If you’re looking for a payroll service for your business, consider the price, vital features and functions, plus whether there’s a free product trial and demos so you can test run and see if it matches your needs.

Here’s a list of the best payroll software for small businesses to get their taxes, benefits and other withholding calculations correct to the penny.


What is the best software for payroll for a small business?



This is an award-wining cloud-based accounting software that’s used in more than 180 countries across the world, and is designed for small and medium-sized businesses.

Its functionalities include invoicing, inventory management, bank reconciliation, expense management and payment of bills, project tracking, multi-currency capability, business performance dashboard, sales tax calculation, and mobile apps, among others.

The unique things about this payroll software for small businesses is that it processes and runs payrolls, while adjusting taxes automatically. It is also very secure what with its multiple approvals and two-factor authentication so fraud is minimized, plus each transaction has details such as dates, users, actions performed and notes.

With Xero, you can get a summarized report of your financial activities, and keep detailed records of all your transactions including tax status, committed quotes, and purchase costs.

Get Xero



Previously known as ZenPayroll, this tool is a cloud-hosted software that combines payroll, administration of benefits, human resource and compliance capabilities in one simple package.

The software is built for small businesses that want to manage their payroll system and HR needs, and it handles this by streamlining and automating calculation, payment and submission of the payroll taxes, while ensuring your business is fully complaint to avoid critical errors.

It doubles up as a HR solution to manage your team without all the paperwork, emails and spreadsheets, and keeps all employee data synced.

Among its advantages include elimination of human errors, full compliance with HIPAA, ACA and ERISA standards while checking data automatically to prepare reviews, send notices and maintain employee privacy.

It also simplifies the management and administration of benefits, employment tax reporting, payments, workers’ insurance, and budget plans, and you can set up and/or manage 401(k) plans easily. You’re also not tied to using it, and you can test run it with the one-month free trial to see if it’s a good fit for your business.

Get Gusto


Sage Intacct

This accounting software is based on a merger by Sage Group and ERP solutions, who bought Intacct, a 19-year old software accounting company. This merger combines the expertise, experience and world-class quality of Sage, the result of which is Sage Intacct, a comprehensive accounting and payroll system.

With this payroll software for small business, you can manage cash, purchases, billing, vendors, revenues, contracts, projects and funds, inventory, and subscriptions, while generating financial reports, all through the cloud system.

It is both flexible and accurate in a bid to improve your business performance and employee productivity in the long run.

The benefits of using this tool include HR accounting which covers aspects such as payroll, benefits, time tracking, and insurance with its single, connected payroll system in different locations to give a view into your payroll structure, its performance, and activities therein.

It is also recognized by AICPA (American Institute of Certified Public Accountants) as a top financial apps provider with numerous industry awards to its belt. Additionally, it has a wide range of accounting capabilities, and you can use built-in report templates to create reports that are configurable and analyze your business’ performance, track sales, and much more.

Get Sage Intacct


Intuit Payroll

Used by more than a million businesses across the world, Intuit payroll software for small business is one of the top products from the company Intuit, besides the famous QuickBooks, and TurboTax.

This platform delivers a worry-free solution for small businesses in terms of managing the payroll system, and lets accountants and owners make payroll efficiently with high accuracy levels, while automating calculations such as tax, and generating paychecks.

Being part of Intuit’s accounting software range, it integrates with QuickBooks for a more robust accounting system, hence your cash flow is improved by making sure your staff are properly and accurately compensated.

Beyond payroll, this software offers employee management tools for hiring top talent, and complying and keeping with labor and hiring laws.

Its benefits include easy and quick management of payroll, free paycheck calculator for both hourly and salaried employees, world class support, plus automatic creation of paychecks once you key in the hours and/or approve staff salaries.

Get Intuit Payroll



This payroll software for small business doesn’t have advanced features and add-ons as the others listed here, but its pricing model is simple, and it offers straightforward necessities for small businesses.

Among its features include unlimited pay runs, tax filings, deposits, and check printing, plus a mobile-friendly system that’s easy to use and quick. You can run your payroll in minutes, and its simple interface makes entering payroll elements like hours, tips, bonuses and reimbursements a walk in the park.

It also has fast load times even on mobile phones and tablets, plus you get a preview pane to view your pay runs to avoid critical errors that can land you penalties from the tax man.

Other things it can do for you include covering compensation and insurance, as the software is a licensed health insurance broker, with fully integrated 401(k) plans. You can also perform HR functions such as employee self-onboarding to save time, automatic new hire reports to the government on your behalf, lifetime accounts which employees can access long after they leave your organisation, online access for employees, guaranteed payroll compliance and automated payroll taxes.

It also works with any employee type, and if you or your employees prefer direct deposit, pre-paid debit cards or doing your own checks, it is possible to pay without any added costs. If you need assistance, OnPay’s Certified Payroll Professionals are on standby to assist via phone.

Get OnPay

Is there a payroll software for small business that you use and it is really helpful? Share with us in the comments section below.


Editor’s Note: This post was originally published in May 2018 and has been since updated for freshness, and accuracy.