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Best Payroll Programs for Small Businesses

Good payroll software is essential for today’s small businesses. But with dozens of options on the market and a wide range of prices and features, it can be difficult to know which payroll program works best for your small business.

Today, we’re going to help you find the best payroll programs for your unique needs. Discover the best payroll program features by reading through the list below.

Top 4 Best Payroll Programs For Small Business

Intuit Online Payroll – Payroll Program

Intuit Payroll Free Trial

There’s a reason that Intuit Online Payroll is at the top of these types of lists all over the internet. It’s the first payroll software that comes up on Google Search for good reason: it’s the world’s most popular online payroll software available today.

Part of the popularity of Intuit Online Payroll is that it syncs perfectly with Intuit QuickBooks, which is easily the world’s most popular accounting software.

Yes, most of the other payroll systems on this list is also specially designed to work with QuickBooks, but Intuit Online Payroll is the cream of the crop in terms of compatibility.

Some of the best features of Intuit Online Payroll Program on your small business include:

Competitive Pricing: Plans start at just $20 per month for the first 6 months, and you add $2 per employee per month. However, most small business owners pay for the Intuit Online Payroll Enhanced  subscription, which is priced at $31.20 per month. The Enhanced version lets you automatically submit taxes and IRS forms through the program. In any case, Intuit Online Payroll is incredibly affordable.

Full Payroll Tax Support: Intuit will handle all of your payroll tax responsibilities. The program calculates your payroll taxes and automatically withholds the correct amount from each paycheck. It also lets you file your payroll taxes with the state and federal government without worrying about manual double entry.

Full Service and Accuracy Guarantee: If you subscribe to Intuit Online Payroll’s full service package, then you’ll receive a guarantee that your taxes will be filed on time and in the correct amount. If an error is made, then Intuit will pay any tax penalties incurred by your small business. Few other companies back up their service with a guarantee like this.

User-Friendly Interface: For the most part, the payroll solutions on this list is easy to use and has a nice UI. However, Intuit Online Payroll may be the easiest to use out of them all. Intuit Online Payroll’s interface is similar to QuickBooks – so if you’ve grown accustomed to the QuickBooks interface over the years, then this should be an easy adjustment.

Full QuickBooks Integration: Everything in QuickBooks automatically syncs with everything in Intuit Online Payroll, which means double entry is a thing of the past. Every time you submit a payroll to run, all of your payday info (like check amounts, state and federal taxes, and deductions), is sent to a server in the cloud. Then, Intuit syncs that information via the cloud to your QuickBooks account. Most of the other payroll programs for small businesses also sync with QuickBooks, although you may have to press an extra button or pay a small extra amount.

Customer Service: Intuit is the world’s largest small business accounting software company, so it has extensive customer support. Customer service is available from 6am to 6pm PST, Monday through Friday as well as 6am to 3pm PST on Saturday. It’s not quite as good as 24/7 support, and it’s not as good as OnPay’s famous customer service, but it’s good for working during normal business hours.

Free Trial: not convinced by any of the other Intuit Online Payroll benefits listed here? The company also offers a free 30 day trial. That trial doesn’t really work like a normal free trial: you just sign up for Intuit with a full standard account membership and you get your first month free.

Downsides – Limited Extra Features: Ultimately, the only real downside to Intuit Online Payroll is the company’s limited extra features. If you want basic payroll software that works for a small to mid-sized business, then Intuit Online Payroll is excellent. But if you want payroll software that has bonus features like human resources guidance, employee retirement plans, health care benefits, and other extras, then Intuit Online Payroll isn’t great (the only bonus features are workers’ compensation plans, a time-tracking feature, and a system where you can buy labor law compliance posters for the office.

At the end of the day, Intuit Online Payroll is the world’s best for a reason. It won’t be a perfect fit for all companies – especially larger companies with more complex needs. But it’s a competitively-priced solution for small and medium businesses.

FreshBooks – Payroll Program

Freshbooks Free TrialFreshBooks may be Intuit’s biggest competitor in the small business accounting software world. Although it’s not strictly payroll software, it is full-featured accounting software that integrates particularly well with ZenPayroll.

FreshBooks has many of the same features as Intuit Online Payroll – including excellent QuickBooks integration. It also has good Android and iOS apps, 256-bit encryption (which is useful if you’re doing payroll anywhere outside the office).

Some of the other notable features with FreshBooks Payroll Program on your small business include:

More than Just Payroll: Yes, FreshBooks integrates with ZenPayroll for easy payroll management. But it’s primarily accounting software. You can use FreshBooks to manage all the bookkeeping aspects of your small business, including invoicing, expenses, time tracking, reporting, and payments.

Gets Along with Other Platforms: FreshBooks is friendly to more than just Intuit’s software. You can connect your FreshBooks with PayPal, MailChimp, Gusto (formerly known as ZenPayroll), and Basecamp, among other platforms.

Free Trial: Like many of the other payroll programs listed here, FreshBooks has a 30 day free trial period. Unlike other payroll programs, however, you don’t need to enter your credit card to enjoy this free trial.

Enhanced Security: FreshBooks comes with 256-bit encryption, which is important if you like to do your accounting anywhere outside of the office (like on mobile devices or on a laptop at a coffee shop). In addition to 256 bit encryption, FreshBooks stores all of your information on its cloud servers, where the data is “Safe, secure and always backed up” according to the official FreshBooks website. These are also the same data centers that host information for General Electric, Cisco, and Pfizer, among other big companies.

Competitive Price: If you just need to manage a single client, then FreshBooks is free permanently. You’ll need to upgrade to the $19.95 per month Seedling subscription, however, to support up to 25 clients.

Downsides – You’ll Need to Pay Extra for Payroll Support: The main downside of using FreshBooks as your payroll program is that it isn’t strictly payroll software. You’ll need to subscribe to a service like Gusto (ZenPayroll) and connect it to FreshBooks in order to manage your business’s entire accounting and payroll departments from the software. ZenPayroll costs $29 per month plus $6 per employee.

If your small business needs to find a payroll program in addition to accounting software, then FreshBooks can be a good choice. If you already use something like QuickBooks, however, then you’re better off using something like Intuit Online Payroll program.

Gusto – Payroll Program

GustoFormerly known as ZenPayroll, Gusto is the rebranded version of the popular payroll software. Gusto is competitively-priced and can easily scale to meet the needs of your small business. It integrates well with both FreshBooks and Intuit QuickBooks – so you probably won’t have to change your existing bookkeeping system.

Gusto also has automatic tax calculations and filing capacity. Its mobile apps and excellent web interface ensure you can access it from any device.

Some of the most popular features of Gusto/ZenPayroll Programon your small business include:

Competitive Pricing: Gusto is relatively cheap, priced at $29 per month plus $6 per employee per month. That makes it slightly more expensive than Intuit Online Payroll but still lower than most payroll software. As you’ll learn below, Gusto also includes many features that are not standard on other payroll software providers.

No Charges for Extra Features: Extra features included in your Gusto subscription are things like direct deposit, year-end tax forms, unlimited payroll runs, year-end W-2s and 1099s, and new-hire reporting.

User-Friendly Interface: Many people prefer the Gusto interface over bigger competitors like Intuit Online Payroll. When you log into your Gusto account, you’ll see a “to do” list along with important updates and upcoming activities. You can also easily add things like hours worked, or garnish an employee’s wages with bonuses.

Strong Customer Service: Gusto has friendly, effective customer service according to most reviews online. The one thing that distinguishes Gusto’s customer support from competitors, however, is its treasure trove of information online in the form of tutorials, webinars, videos, etc. With other payroll programs, you might have to contact companies like Intuit to get your questions answered, while with Gusto it takes only a few seconds of searching.

AutoPilot: Don’t feel like doing payroll this week? Gusto has a popular AutoPilot setting that lets you tell your system to automatically process payroll each pay period, then sends you a notification when payroll is completed. If there have been no changes between payroll periods, then this is a great advantage.

Available Across America: Formerly, ZenPayroll was only available in 26 states. Today, the re-branded Gusto now works across America and can accept employees from across the country.

2 Month Free Trial: While most competitors – including Intuit Online Payroll – have a 30 day free trial, Gusto has a popular 2 month free trial.

Downside – It Doesn’t Include All Features: Some of the features not included with Gusto are human resource-like features, including health care benefits and employee retirement plans.

Ultimately, Gusto is the best alternative to Intuit Online Payroll when it comes to payroll programs. It’s full-featured and includes popular benefits like AutoPilot that can make running your small business’s payroll a breeze.

OnPay – Payroll Program

OnpayOnPay is an excellent choice for very small businesses (businesses with fewer than 12 employees). At this number of employees, few payroll programs are cheaper than OnPay. Aside from its low price tag, OnPay is also popular for its extensive customer service options.

Here are some of the benefits of running OnPay payroll program on your small business:

Competitive Pricing: OnPay charges a base rate of $40 per month. That’s a more expensive base rate than the other payroll programs listed here. However, OnPay’s base rate includes 10 employees. Beyond that, you pay $1 for each additional employee. That’s significantly cheaper than Gusto’s $6 per employee rate and even Intuit’s $2 per employee rate (especially considering that these services don’t include any “free” employees”).

Full Tax Services: OnPay handles all of your payroll taxes for you, just like good payroll software should. After calculating your payroll taxes every month, the software will then process the required payments to all applicable local, state, and federal agencies.

Quarterly and Annual Payroll Returns: The software also automatically prepares and files quarterly and annual payroll returns for your business.

Guarantee: If OnPay makes any mistakes while filing your taxes, it will take full responsibility for any penalties incurred. So if your taxes aren’t paid accurately or on-time, then OnPay will fix that problem for you.

Customer Service: OnPay’s customer service is distinguished by its long hours – including long office hours all weekend. This may not seem like a big deal, but few of OnPay’s competitors have such generous customer service hours. Customer service lines are open from 9am to 8pm Monday through Friday. There’s also an emergency support line open from 9am to 8pm on Saturdays and Sundays.

Mobile Friendly: Run payroll from anywhere with OnPay’s excellent Android and iOS mobile support.

Downsides – Not Quite as Full Featured as Some Payroll Services: OnPay’s few limitations include the fact that it doesn’t have the same wide variety of service offerings as its competitors, including health care benefits or employee retirement plans.

Some people believe that OnPay is one of the newest members of the payroll program industry – OnPay was only launched in 2011. However, OnPay’s parent company is named Payroll Center, Inc., and that company has over 30 years of experience in the industry. In other words, you’re not working with a payroll rookie when you sign up for a payroll program like OnPay.

About Johnson Hur

After having graduated with a degree in Finance and working for a Fortune 500 company for several years, Johnson decided to follow his passion by embarking on a path to the digital world. He has over 8 years of experience with large companies setting marketing strategy.


  1. Slickpie(www.slickpie.com) is an online free accounting software. The invoices are super easy to create. It helps me keep track of income and expenses in a clean and intuitive. It links with my bank accounts and credit cards, gives me professional invoicing and track all of my taxes.

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