Payroll Software: Key Considerations Before You Pick

Payroll processing tasks are simple and hassle-free to complete if you’re using a great software solution. Using payroll software to handle your basic tax and payroll responsibilities increases your workplace efficiencies, reduces errors and saves time, so you can implement big-picture strategies and programs for the office. Learn more about the benefits of using payroll software, features to look for and the top payroll software programs for small businesses. 


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Benefits of using payroll software

A payroll software system is an online platform that automates the entire payroll process by completing basic actions like calculating your payroll, creating tax statements and distributing employees’ paychecks. You’re able to handle payment and tax information for full-time, part-time and contract employees. Common benefits of using a payroll software to handle your payment processes include:


  • Automates and streamlines the payroll process: Payroll tasks that your accounting and human resources teams once completed by hand are all completed within the system. This makes the payroll process more efficient and streamlined, as it automatically inputs your company’s information and completes all the calculations for you. 
  • Allows you to manage your payroll from anywhere: Most payroll services have online portals or applications for you to access from your mobile phone or any other device, making it easy for both you and employees to quickly log in and view or edit any payroll information.
  • Reduces user error: Automatically updating payroll information and allowing employees to log in and edit their information reduces the user error that used to be caused by manually inserting payroll information.  
  • Gives you more time to focus on big picture items: Since the system automatically updates and handles payroll information, this frees up your time to focus on larger work items like building strategies to strengthen the company’s operations and increase performance levels.  


Related: How to Hire a Payroll Specialist


Features to look for in your payroll software

Picking the best payroll software for your business depends on the features your business needs to successfully complete its payroll processes. Features to look for in your payroll software include:


Local, state and federal tax filing 

Most payroll systems handle a large majority of your tax information and filing. Many tax-related duties a payroll software completes include:


  • Filing quarterly payroll tax reports 
  • Paying employee tax withholding fees to the respective local, state and federal entities
  • Providing the necessary W-2 and 1099 forms to the designated parties at the end of the year 


Sick leave and PTO tracking

Most payroll systems have employee portals for team members to easily sign in and input or request information. Employees can request vacation days for their manager to easily access, review and approve directly from the platform. Employees also view how much of their paid time off and sick leave is available to help them plan their vacation schedules accordingly.  


New-hire report documentation 

Onboarding is much easier when using payroll software, as it usually stores new hire documents for employees to easily locate and sign inside of the platform. It then stores it in the system for you to retrieve when needed. The payroll software also tracks your new hire numbers and reports this information to the state, leaving that task off your to-do list. 


Direct deposit for employees

Rather than manually completing the process of mailing paychecks to your employees, the payroll software allows you to transfer employee’s paychecks directly into their bank accounts on payday. Gather employees’ bank account information by having them input it into the secure payroll software system. 


Related: What is Competitive Pay?


Self-service employee portal

All members of your company have easy access into the payroll software system by creating an account and logging in. Employees view and update their personal information on tax forms and other employee documents. They’re also able to pull their pay stubs as needed from the portal. Update the preferences to give designated people access to different parts of the payroll system. This keeps certain employees from viewing private company or employee information. 


Third-party integrations 

If you have other HR software you currently use to store employee or bookkeeping information, check to see if it integrates with your payroll software. Being able to integrate with other systems saves you time, streamlines your processes and helps you avoid making any mistakes when transferring important employee and company information. 


Benefits information and documents

Your employee’s benefits documentation and information is stored on the payroll software, allowing them to easily log in, access and view the benefits offered to them. Employees can easily view their health insurance information through the portal. Some payroll software systems even let them choose which insurance plan they’d like to opt in for straight from the platform. 


Top payroll software available for small businesses

After better understanding which features are best for your business to use, start reviewing different payroll software options to find one that includes all the tools you’re searching for. Top payroll software for businesses to use include: 


Intuit Quickbooks 

If you’re currently using Quickbooks accounting software, this payroll system could be a good option as it’ll easily integrate your information stored in other Quickbooks applications. It offers tutorials to carefully walk you through using this program. You’re also able to run payroll as much as needed with no extra cost. Your employees can easily view and access their pay stubs, PTO balances and tax information. It also includes TSheets time tracking for employees to easily log their time for managers to review. 


Though it integrates with other Quickbooks applications, there are very few outside third-party integrations it collaborates with. Their customer service is also difficult to reach if you’re facing any unexpected or significant errors with the software. 


Prices per month

  • Self-employed: $4.50
  • Simple Start: $7.50
  • Plus: $21
  • Advanced: $45


Patriot Software

This software gives you access to unlimited pay runs and electronic tax payments and filings to make the tax process easy to complete. Employees use the online portal to sign in and check their paystubs for compensation information or update their bank account details. It also includes time-tracking add-ons and additional HR software that electronically stores your files and other employee information.


Processing payroll takes longer than other software systems as it requires a four-day lead time for direct deposits, so try to plan ahead to account for the extra time. You may also receive additional up-charges and in-app purchases to use any additional features that are often free on other systems.


Prices per month

  • Basic payroll: $10
  • Full service payroll: $30


Related: How to Hire a Payroll Manager


ADP payroll

This software is also an effective solution for those planning to expand their business significantly over the next few years. It offers basic payroll software features, including electronic tax payments, automatic tax filing at the end of the year and direct deposit. Professionals stay updated on state and federal laws to ensure your vacation time and leave programs remain compliant. It also integrates with numerous third-parties.


You may be charged extra for setup fees. It can also be difficult getting ahold of customer service during certain hours of the day. 


Prices per month

  • Core payroll: $59 plus $4 per employee
  • Enhanced payroll: Pricing specific to your business
  • Complete payroll and HR: Pricing specific to your business
  • Pro Payroll and HR: Pricing specific to your business



If your small business has been around for a few years and is consistently growing, you could benefit from using Paycor software. It offers many HR tools to increase your efficiencies when managing job applications, training documents and employee performance ratings. There are several people management tools available, like benefits information, onboarding materials and a PTO tracker. 


You’re unable to edit your payroll once you submit it. so make sure your payroll is accurate before submitting. Some employees also find it difficult to edit their time off approvals and requests within the system.


Prices per month: 

  • Basic: $99 
  • Essential: $149
  • Complete: $199



This service provides you with a systems staff member to assist you through the setup process, address any compliance issues and resolve any of your other system needs or concerns. The software contains several payment options for employees like checks, direct deposit, payroll on-demand and pay cards. It also contains a convenient mobile app you can access whenever you need to view any time-sensitive information. This system integrates with a wide variety of third party platforms.


It doesn’t handle time-off requests and PTO tracking, so those need to be reviewed and tracked manually or by another system. Benefits information is only available if you purchase it separately. 


Prices per month

  • Paychex Go: $59
  • Paychex Flex: Pricing specific to your business
  • Paychex Flex Enterprise: Pricing specific to your business


Take your time when picking the best payroll software for your business by carefully weighing the pros and cons. Meet with your staff beforehand to learn their preferences and needs to ensure you select a software that benefits your entire team.

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