Best in-house payroll software for a small business in 2025
List of best in-house payroll software for small businesses
What is payroll software?
Payroll software is a specialized program designed to automate and manage employee payments. This type of software often handles payroll tax management as well.
As globalization becomes the norm even for small businesses, payroll management has become increasingly more tedious.
Today, it’s common for a small business owner in the US to have an accountant from the Philippines or a web developer from India. Having these offshore workers adds a layer of complexity to payroll management as currency conversions and international tax regulations have to be considered.
This precipitated the need for specialized software to solve the difficulties that a global workforce presents.
Why small businesses need payroll software
Using payroll software can help small businesses in many way:
Automating payroll saves time
Small business owners spend an average of five hours a week doing payroll-related tasks. While it may not seem like much, this adds up to a considerable 260 hours annually, or 10 days every year.
By using specialized software to automate payroll management, business owners can instead use the 10 days they saved on activities that can generate revenue, such as developing marketing campaigns.
Using payroll software promotes transparency
Another benefit of using payroll software is the morale boost it gives employees.
With an automated payroll system, workers are assured they’ll receive accurate pay on time and without having to go through the hassle of submitting and double-checking attendance records.
The same goes for business owners and HR departments. As payroll software often handles PTOs, attendance, and hours worked, a great chunk of responsibilities is taken off their shoulders.
Payroll software reduces errors
As with all automated systems, payroll software significantly reduces the chances of errors in processing payrolls and salary taxes.
By removing human errors from the equation, small business owners eliminate the possibility of inaccurate data entry, accidental deletion of formulas, and other common sources of payroll mishaps.
Payroll software makes compliance easier
Perhaps one of the most helpful aspects of using payroll software is how it makes compliance easy and convenient.
With an automated payroll solution, small businesses no longer have to worry about incurring hefty penalties for non-compliance or incorrect filing of taxes.
Since these types of software keep detailed records of all payroll-related transactions, it becomes much easier to audit and be on top of bookkeeping regardless of local, state, federal, or even international regulations.
Payroll software for a small business: What to look for
As businesses worldwide began to realize the significance of payroll software, many tech vendors capitalized on the profit opportunities it presented and started to develop and sell their own.
If you’re looking for a payroll solution for your small business, here are some key features you should look for to make sure you get the most bang for your buck:
Automated payroll computation
This should go without saying, considering that automatic processing of payroll is the whole point of payroll software.
Payroll computation should include both deductions (e.g., social security contributions, taxes, etc.) and other compensations.
Tax compliance tools
Payroll management goes hand in hand with taxes. It’s essential to look for payroll software that provides access to tax compliance tools, or, even better, automatically handles that aspect for you.
Employee self-service
Payroll solutions that let your employees self-serve (e.g., view their pay slips, check and update personal information) are another must-have feature.
This empowers your workers and gives them access to payroll without having to go through HR and even while on the go.
Scalability
Similar to other automation programs, one of the true tests of greatness for payroll software is how well it can scale. A reliable payroll solution should be able to handle 200 employees as smoothly as it manages 50.
Integration with your existing technologies
Lastly, the payroll software you should look for is one that wouldn’t break your existing HR infrastructure. Always check if a payroll solution is capable of integrating with your other software.
It would be counterproductive to automate your payroll system at the cost of overhauling other perfectly good processes.
Best in-house payroll software for small businesses
1. Deel
Deel is an international payroll software that offers speed, flexibility, and compliance combined with a 24/7 accessible support team. Supporting payroll processing in over 120 countries, Deel Payroll is one of the most-used payroll software globally.
Aside from its unified payroll and HR, one of Deel’s selling points is its active monitoring of regulatory changes. This feature lets businesses stay on top of compliance needs before they become an issue.
Pricing: From $29 to $599 per employee per month
2. QuickBooks
QuickBooks lives up to its name with its payroll software that can finish doing your payroll in just under five minutes (after the initial setup).
Users don’t have to worry about any complexities or steep learning curves when using the QuickBooks software. The company’s in-house experts will assist them from the initial setup to even managing taxes.
Another perk of using this payroll management software is the tax penalty protection, where QuickBooks will cover up to $25,000 if users receive a tax penalty for any reason.
Pricing: $25 (plus $6 per employee per month) to $65 (plus $11 per employee per month)
3. Gusto
Gusto is a highly rated payroll software with automatic tax management and seamless integration with other data HRs need to manage (e.g., 401k, time tracking, and PTO).
For US employers with local employees, Gusto assures tax registration in all 50 states.
Handling the payroll and compensation of offshore workers is also made easy with Gusto Global. Acting as Gusto’s Employer of Records (EOR) service, Gusto Global lets companies easily manage global teams and pay them in their local currencies.
Pricing: From $49 (plus $6 per person per month) to $135 (plus $16.50 per person per month)
4. Patriot
Trusted by more than 60,000 customers in the US, Patriot’s payroll software is made for businesses with up to 500 employees.
Patriot’s online payroll management system stays true to its name with its unrivaled customer support within the US. The software’s speed is also commendable, with its ability to process payroll in under three minutes.
With its simplified steps, users will find using the Patriot software to be no challenge: they only have to enter hours, approve the payroll, and print.
Pricing: $8.50 (plus $2 per employee per month) to $18.50 (plus $2.50 per employee per month) plus optional add-ons
5. Netchex
Netchex offers automatic tax filing and flexible payment options for employees, including standard checks, direct deposits, and pay cards.
This payroll software has multiple integrations that make compensation management easier, such as:
- Hours and attendance
- Benefits administration
- Employee self-service PTO
The Netchex payroll software also has pre-processing reports for added accuracy and error-free rollout of salaries.
Pricing: Available upon request
6. Paychex
Made by a payroll and HR solutions company, Paychex’s online payroll software lets companies pay employees in just a few clicks.
Paychex’s small business payroll services have 24/7 customer support and automatic computation, payment, and filing of payroll taxes. It also allows employees to initiate self-service actions for more convenience.
Pricing: Available upon request
7. Remote
Pay anyone, anywhere—that’s what Remote’s global payroll software offers. Remote’s software makes it easier for businesses to stay compliant with tax and payroll regulations, even across national borders.
This is especially helpful for small businesses hiring offshore staff for lower costs, as cross-border payroll can be expensive and complex. With Remote’s EOR service, employers with remote workers no longer need to have a local business entity in their employees’ country.
Pricing: $29 per employee per month
8. Square
Square is an easy-to-use payroll software with lots of integration, even with other third-party payroll solutions.
Aside from its automated filing of payroll taxes, Square’s software also handles payments to W-2 employees and 1099 contractors.
Pricing: From $6 per person paid per month to $35 plus $6 per person paid per month
9. OnPay
OnPay is a multi-awarded payroll software for small businesses. Recognized by CNN, Business.com, CNBC, and other organizations, OnPay’s streamlined payroll and HR software handles employee payments and helps simplify the HR tasks of small businesses.
OnPay doesn’t charge fees for integration or implementation. It also offers support through phone calls, chat, and email.
Pricing: $40 plus $6 per person per month
10. HomeBase
Serving over 100,000 small businesses in the US, HomeBase is a trusted payroll software with numerous awards and recognitions to back its claims.
HomeBase handles not only payrolls but also all the administrative tasks and paperwork that come with it, so companies can focus on their core activities.
One of HomeBase’s advantages is letting employees have earned wages access, a feature that allows workers to basically “withdraw” payments they’ve already earned, at no additional cost to employers.
Pricing: $39 plus $6 per employee per month
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