Apply For Financing

Best Payroll Software for Small Business Owners

For many small business owners, employee payroll can be a massive headache.  Figuring out benefits deductions, federal, state and local taxes and other complicated aspects of payroll can be incredibly stressful and needlessly complex.  This is why payroll software can be such a good investment.  While the upfront cost of a decent payroll software program can be high, it typically pays for itself in short order.  When you have a good payroll software program running, you can focus on running and growing your business — not on the intricacies of onboarding new employees or tax filings.


There are numerous payroll software options out there, each with its own advantages and disadvantages.  The best payroll softball will depend on your small business’ size, type and budget.  Read on to learn some more about some top choices for small business payroll software.

Budget Payroll Software

Many small businesses have a limited amount of money to spend on payroll software, which can often be pricey.  For small business owners on a budget, there are two great options when it comes to payroll software.


OnPay allows small businesses with up to 10 employees to manage their payrolls with automatic payroll deductions and tax payments.  OnPay gives business owners guaranteed accurate and timely tax filings and payments. Because OnPay is a cloud-based system, it can be managed from anywhere with an internet connection.  OnPay costs $39.95 per month for up to 10 employees, with additional employees costing $1 per month.  The major downside of OnPay is that direct deposit is not included in its base price.  Direct deposit costs an additional $8 per month. For businesses that want to provide their employees with printed and mailed W-2 forms for tax purposes, OnPay charges an additional $3.75 plus shipping.


If you have more than 10 employees, then Patriot Software may be the better choice for your smaller business.  Patriot Software allows small businesses with up to 100 employees to set up payroll, with full-service options including printed or direct deposit checks, automatic tax filing, guaranteed on-time tax payment and filing of W-2 and W-3 forms.  This full-service payroll plan costs just $25 per month, plus $4 per employee for up to 5 people.  Patriot Software offers discounts based on the number of employees on your payroll, so the best way to calculate your total monthly cost is to use its website calculator to determine what your cost based on your number of employees.

Quick Integration Payroll Software

If your main goal with payroll software is to get up and running quickly, then SurePayroll may be the best option for you.  This software provides automatic filing and payment of local, state and federal taxes.  Online enrollment into the system takes just 10 to 15 minutes to complete.  According to SurePayroll, once you are established in the system, you can process your payroll within five business days.


SurePayroll bases its pricing on the frequency of your paydays and the number of your employees.  Pricing starts at $49 per month, plus $5 per employee per month.  If you have more than 10 employees, monthly fees start at $99 per month.  SurePay charges additional fees for end-of-year filings, such as W-2 and 1099 forms.

Apply For Financing

Best Overall Payroll Software

For larger business, QuickBooks Payroll by Intuit is a great choice for anyone who needs a more full service option.  QuickBooks Payroll guarantees mistake-free paychecks and payroll taxes, and will take care of tax payments for your small business.  With this software package, technicians will assist you from start to finish in setting up the software, inputting information, and filing and paying taxes.  If you already use QuickBooks for your accounting software, QuickBooks Payroll is a natural choice, as it will easily integrate with your small business’ existing platform.


Of course, this level of service comes at a price:  QuickBooks Payroll starts at $64 per month, plus $2 per month per employee for the first six months.  After the first six months, the rate jumps to $99 per month, plus $2 per employee.  If you have a significant number of employees, these costs could add up quickly; a business with 50 employees would pay $199 per month after the first six months.

As an alternative to QuickBooks Payroll, Gusto (formerly ZenPayroll) offers a full complement of features for automatic payroll.  Through this software, employees can perform the onboarding process by themselves, which can save substantial time.  New hires simply log in and enter in the pertinent information, such as their social security number and bank account information for direct deposit.  This allows Gusto to set them up in the payroll system, report them to the government, get tax filings established and have pay stubs emailed directly to them.  With Gusto, all state, local and federal taxes are automatically filed, and employee benefits can be administered through the software.  Gusto can be integrated with a business’ accounting software, such as FreshBooks, QuickBooks or Xero.


For small businesses Gusto is significantly less expensive than Quickbooks Payroll, and serves business with between one and one hundred employees.  The software costs $39 per month, plus $6 per employee.  In the example above, a company with 50 employees would pay $339 per month.  However, a company with just 5 employees would pay $69 per month.  That makes Gusto an ideal choice for companies with a limited number of employees.


While payroll software can be a pricey addition to your monthly budget, it can be a significant time saver, making it a worthwhile investment. Consider a number of factors when deciding what payroll software will work best for your small business, from the number of employees that you have, to the amount of assistance you will need to run the software, to the need to integrate your payroll software with your other software.  By making a smart choice on your payroll software, you can make your life as a small business owner a lot easier — and more efficient!