Payroll software helps businesses scale

Payroll software should make it easier to run ⁠— and grow ⁠— your business. Providers should handle the hard stuff so you can spend more time on what’s most important.

What you’ll learn

Fast facts about payroll software

    • Most software allows employers to pay employees with their preferred method including for direct deposit, debit card payments, or printing physical checks
    • Payroll software tools typically come with built-in self service so employees can access pay stubs, download W-2s, 1099s, review withholdings or request time off
    • Providers should withhold federal, state, and local payroll taxes each pay run and make your tax payments


What is payroll software?

Payroll software helps employers pay employees accurately and on time while automating tax filing for compliance. It eliminates the need for manual calculations, saves time, and ensures the correct deductions are made. With centralized employee data, it generates essential documents like pay stubs, and automates direct deposit paychecks.


Payroll software saves time

Most businesses use payroll software to minimize administrative hires, streamline operations, keep compliant, and free up time to focus on growth. Because some companies hire a mix of W-2 employees, independent contractors, and part-time workers, modern providers make it easy to pay individuals, no matter how they are classified.



Are there free payroll software options?

Free payroll software does exist, but it depends on the type of functionality you’re looking for. In most cases the top tools are going to require an investment.


Where do you use it?

Payroll software is typically available in the cloud, which means you (or employees with access) can log in and use it securely from internet browsers like Chrome, Firefox, or Safari, as well as mobile devices. There are applications, on the other hand, that are installed on your laptop or computer workstation (that don’t need internet access to use).

“Ask for help: Working with a payroll software company like OnPay can be a smart move to ensure compliance with tax laws and regulations.”

— Noel Lorenzana, CPA and tax expert


Picking the best payroll software for your business

Business owners researching payroll solutions have a lot of choices. So how can you be sure you’re choosing the right payroll software that checks all the boxes? Both third-party reviews  and the first-hand experiences of other businesses. Want to learn more? Read reviews of our software by the top media outlets or check out comments from similar businesses that have chosen us as their payroll provider.


Can a payroll solution save me time?

OnPay’s research found that small businesses spend almost 40 hours a month on payroll and HR-related tasks. Though there are many factors that affect a small business, incorporating a payroll solution can reduce time spent on administrative work and back-office to-dos. Some businesses take the reins when running payroll. For an overview of what this entails, read our guide on how to do payroll yourself.

References factor in

Almost 40% of small businesses say positive reviews, testimonials, and recommendations from trusted sources (colleague or friend) are important part of their research when looking for a payroll software provider.

Source: OnPay small business market survey


Payroll tax filing should be standard

It’s important for business owners to stay on top of tax compliance. That’s why, in addition to filing and paying your federal payroll taxes, most software tools should take care of state and local payroll taxes, without additional fees (no matter how many states you operate in). Most companies should make your tax payments, and file Form 941 quarterly and Form 940 at the end of each year. Check to see if you’ll have lifetime access to records of these filings stored right in your account (no matter the provider), so you always know which tax form filing has been taken care of and when.


We make switching payroll software ridiculously easy

“It was very easy to switch from another provider to OnPay. The interface is user friendly and I was running payroll in no time.”


– Luke, Daily’s Produce


Ask about accounting integrations

Because employers need to include payroll data in their general ledger, manual entry can be time-consuming and subject to errors. That’s where accounting integrations come in. Most software providers should have integrations accounting software such as Xero and Quickbooks. If you’re curious about the ones that OnPay offers, you can see all integrations here.

Payroll software search

Nearly 40% of small businesses look for payroll software that includes HR, benefits, and other features.

Source: OnPay small business market survey

Designed to be accurate for everyone


Ask what payroll reports you can run

In many cases software should have a report designer you can customize (so you can create a custom view that works best for your needs). For example, being able to filter by employee type, location, or department is something that comes out-of-the box. Our software has many pre-built templates and you can explore payroll reports here.


The service and expertise you deserve

“OnPay is simple to use and the customer support is outstanding! They have been fantastic in their accuracy and promptness, every time I’ve needed them.”


– Scott, Silicon Valley Golf Performance Center


Why do businesses use payroll software?

Payroll processing can be time-consuming, and needs to be handled correctly for companies to stay compliant. Even the most basic payroll requires close attention to detail. Most payroll software solutions automate the heavy lifting needed to process payroll while staying up-to-date with employment laws related to payroll tax filings and compliance.


What payroll software should do

Though features vary across providers, generally, a basic payroll software system should offer business owners the ability to:

  • Run payroll as often as they like
  • Calculate wages accurately and on time
  • Set more than one pay schedule
  • Withhold payroll taxes each pay run and make tax payments
  • Seamlessly integrate with accounting software plus time-tracking software
  • Pay workers with direct deposit


These are just some of the reasons why businesses incorporate payroll software services into their operations. But there’s more that goes into a great payroll service than just the payroll software system.

Do I need payroll software if I only have one employee?

Yes, most businesses with one employee still need to run payroll, even if that employee is you. This is because the payroll process involves more than just calculating and distributing wages to employees. It also includes keeping track of earnings, withholding taxes, tracking benefits contributions, and providing necessary documentation of payroll records where required. OnPay makes it easier to calculate, pay, and file payroll taxes, even if you only have one employee on the team.


Improve your payroll process prowess

There can be a lot to keep up with when running payroll manually, even with only a few employees. Our payroll experts share their knowledge in resources to help you get things right. From completing your tax forms to keeping payroll operations running smoothly, we break down the tough topics so business owners can quickly find the information you need.

Software should also

More features to ask about

When searching for payroll software, here’s some other considerations before picking a tool.

  • Some companies let you set more than one pay schedule or use different pay rates for individual employees.
  • Deducting garnishments should be something you can do (and be able to set rules for when garnishments should stop). We record them in paystubs and expense reports automatically.
  • Unemployment insurance withholding should be standard for employees’ state and federal unemployment insurance payments. We process your company’s contributions, too.
  • If you have multi-state payroll needs make sure the provide does not have extra fees for handling employee taxes in more than one state.



Award-winning customer service

“OnPay is a great solution for my business. It is an easy, flexible source for managing my employees’ payroll and benefits. And, if I ever have questions or concerns, their customer support is on point.”


– Dain C Paxton, DMD MS LLC


User-friendly for all businesses

“OnPay is a very convenient tool for small business owners like me. It’s quick and easy and allows me to run payroll with what works best for my business.”


– Andrea Gutierrez Ready, Set, Dance! LLC


Use benefits to attract talent

Growing your team comes with growing responsibilities, from onboarding new hires to staying compliant with HR-related issues. In addition to keeping track of a host of administrative tasks, many employers are looking for ways to create a happy and productive workplace. That’s why we stay ahead of human resource trends and publish resources that businesses can use to take their HR efforts up a notch.


It’s easy to get started

Try OnPay out yourself to see how easy payroll and HR can be. To get started, just share a few basic details about your business. Our team of pros will set everything up and import your employees’ information for you.

Small business payroll software FAQs

  • How can I run my own payroll for my company?

    Running payroll requires a few steps, whether using payroll software or running it manually and can be accomplished in six steps. What follows is a high-level overview of the steps, and we go into more detail on each one in our article on how to run payroll for the first time.

    Step one: Get a FEIN.

    Step two: Register with state agencies

    Step three: Register in every state where employees reside

    Step four: Employee forms

    Step five: Create a pay schedule

    Step six: Figure out how you’ll pay employees

  • How long does it take to set up and start using software for payroll?

    Most providers make the software setup a quick process. In many cases, the vendor will need some basic details such as your company name, Tin-house payroll experts will do all the heavy lifting — from setting up your dashboard to adding your clients and their employees. We’ll even enter any prior wages to make it easy to switch. And can have you up and running in a matter of days.

  • What size organizations typically use payroll software to pay employees?

    Businesses of all shapes and sizes use payroll software because it can save time, its affordable, most integrate with accounting software, many are easy to use, and can be accessed from anywhere on the internet, including mobile devices, tablets, or laptops.

  • Am I able to integrate payroll with my accounting software as well as time tracking software?

    We have the very best payroll integrations with QuickBooks and Xero, and our payroll software syncs seamlessly with top time-tracking software, like QuickBooks Time (formerly TSheets), Deputy, and When I Work. See all our integrations.

  • Can you help me with my payroll taxes?

    Good question! While we offer easy-to-use payroll software that’s trusted by thousands of business owners, one-on-one tax consultation does not appear on our list of services. That’s why we make it easy for you to invite your bookkeeper into your payroll process, with advanced permissions that keep you in control of who sees what.

  • How do companies like OnPay keep payroll data safe?

    We use industry-standard SSL high-grade encryption (AES-256 256 bit), housed in our secure data facility. All data is redundantly backed up in real-time in multiple locations in the US. We also allow you to set up Multi-Factor Authentication for your account, with the option to verify your login, either periodically, or upon each login.

  • Why do businesses choose direct deposit?

    It’s the easiest and safest way to pay people on-time, accurately, and with almost no effort. Cash can be lost or stolen, and checks can be misplaced, or even forged, but direct deposit is the most secure way to pay your workers. Learn about our direct deposit payroll.