5+ best small business payroll software [Free & Paid]

by Milan Stanojevic
Milan Stanojevic
Milan Stanojevic
Windows & Software Expert
Milan has been enthusiastic about PCs ever since his childhood days, and this led him to take interest in all PC-related technologies. Before joining WindowsReport, he worked as... read more
Affiliate Disclosure
  • Reliable payroll software can help you keep track of your small business and help you with everything tax-related.
  • If you find it hard to choose a specific tool, we narrow down the options for you with these suggestions, so keep reading.
  • Good tools help you track income and expenses, create estimates, generate paychecks, and more.
  • Many of these suggestions are really cost-efficient and also save you a lot of time while providing error-free tax procedures.
payroll software small business

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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, each 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 are 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 are the best small business payroll services?


QuickBooks is one of the most popular bookkeeping software that supports small businesses, as well as big business environments.

The tool helps to secure data sharing with an accountant and it supports integration with Microsoft Outlook. Besides, it is easy to use anywhere, on any device, and by all the employees that you give access to, including your accountant.

Some of the most notable features include:

  • Mileage tracking –  Get shareable reports that break down miles driven and potential deductions.
  • Track income & expenses- Import transactions from your bank, credit cards, PayPal, Square, and more. For easier use, sort transactions into categories.
  • Create & send estimates – Customize estimates to fit your brand and business needs.
  • Maximize tax deductions – organize income and expenses into tax categories and share them with your accountant to avoid tax surprises.


Use QuickBooks to be up-to-date with how your business is doing with sales, accounts receivable, and accounts payable.

Check priceVisit website


Similarly, with QuickBooks, TurboTax is an app also owned by Intuit, that focuses on facilitating the process of filing tax returns for small businesses.

One of the best things about it is that it’s free to use for certain operations, such as filing your federal and state taxes, importing your return from a previous year from similar tax software, or offering guidance in case of an audit.

With the free account, you also get access to an online community of specialists and customers, where you can share ideas and get informed about various processes.

Furthermore, with the paid plans the software also helps you find the best tax break depending on how you choose to itemize deductions from expenses, auto-import your investment info and tax data, get one-to-one specialized help if necessary, and even turn donations into big deductions.

TurboTax is suitable for both small businesses and self-employed entrepreneurs alike.



Get your W-2 income or EIC situations covered and claim the standard deduction with this user-friendly software.

Check priceVisit website

Intuit Payroll

Used by more than a million businesses across the world, Intuit payroll software for small businesses 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 is 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, a 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.

Intuit Payroll

Intuit Payroll

Manage your business finances efficiently with this advanced payroll solution!

Check priceVisit website

Sage Intacct

This accounting software is based on a merger by Sage Group and ERP solutions, which 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 businesses, 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.

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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.

Sage Intacct

Sage Intacct

Grow your business and manage your finances smartly with this robust ERP software!

Check priceVisit website


This payroll software for small businesses 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 taxman.

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, online access for employees, guaranteed payroll compliance, and automated payroll taxes.

The tool can hold lifetime accounts that employees can access long after they leave your organization.

OnPay 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.



Maximize your productivity and enhance your business with OnPay, an all-in-one payroll tool!

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Previously known as ZenPayroll, this tool is a cloud-hosted software that combines payroll, administration of benefits, human resources, 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 compliant to avoid critical errors.

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

Among its advantages include the 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.

Get Gusto


This is award-winning 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 thing about this payroll software for small businesses is that it processes and runs payrolls while adjusting taxes automatically. It is also very secure 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

Doing your taxes is not an easy task regardless if you are working on your personal finances, or on your business’s finances, and using specialized services can be your best bet.

Is there payroll software for small businesses that you use and it’s really helpful? Share it with us in the comments section below.

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