The Best Payroll Apps for Small Business 2020

Paychex Flex: Best overall

App Store rating: 4.8 stars (112.6K reviews)³
Google Play rating: 4.6 stars (10.5K reviews)⁴

Paychex Flex’s app is far and away the most popular payroll app for small businesses. So what makes Paychex Flex’s app so great? For one thing, it does basically everything the cloud-based payroll software can do.

The software and app also sync effortlessly with each other. If you start entering payroll data on your office laptop but have to take off early to take your child to the doctor, you can pick up right where you left off on your phone in the waiting room.

Employees can use the employee-facing version of the app to access their payroll data, check out their W-2 forms and paystubs, and even tweak their 401(k) contributions.

Paychex recently updated their website to include transparent pricing . . . kind of.

For instance, Paychex’s site now says Express Payroll starts at $15 for weekly payroll runs plus $1 per payee. Seems reasonable, right? It is—unless the $15 charge isn’t monthly but per payroll run. So if you pay your employees weekly, you’d be paying around $64 a month for just one employee.

That puts Paychex’s starting price at $60 a month, not $15, even though $15 is the first number you’ll see listed for Express Payroll. It’s not quite a bait and switch, but it’s definitely less than ideal. Unfortunately, when we tried to confirm with Paychex that their pricing is per payroll run and not per month, we couldn’t get a straight answer from customer service, which doesn’t bode particularly well for future customers.

Square Payroll: Most affordable

App Store rating: 4.8 stars (1.6K reviews)⁵
Google Play rating: 4.5 stars (260 reviews)⁶

The Square Payroll app is super versatile—it’s just as easy to pay your W-2 hourly and salaried employees as it is to pay your contractors. Plus, Square’s payroll app syncs easily with its point-of-sale app; you can import employee and contractor hours and then pay them in just a few clicks.

Want to take payroll off your plate entirely? Square Payroll’s app includes an automatic payroll option. If your salaried workers get paid on a consistent pay schedule and make a consistent rate, automatic payroll keeps things simple and ensures employees are paid—even if you forget about payday completely. (Note that you can choose this option only with Square’s plan for employees and contractors.)

Finally, along with running payroll, you can use Square’s app to track employees’ paid time off (PTO), sick leave, and overtime.

Compared to Paychex Flex, Square Payroll is both more comprehensive and more affordable. Square offers unlimited payroll runs in all 50 states and DC, so you can pay contractors as many times as you need to during the month without paying an additional fee. Plus, the $29 fee is definitely per month rather than per payroll run, which is fairer, easier to budget for, and not necessary to verify through customer service.

And with either of Square’s plans, you can pay employees and contractors via direct deposit or paper check. (Paychex Flex offers paper checks with only its two most expensive plans.) You’ll also get custom reporting, wage garnishment options, tip calculation and importing, and automatic W-2 or 1099 year-end tax form filing.

However, Paychex Flex offers much more comprehensive HR support. If your team has 50+ people, Paychex Flex’s online payroll software could be a better fit. But if you work entirely with contractors instead of W-2 employees, go with Square. Its contractor-only plan doesn’t have a monthly base fee. You pay a $5 fee each time you pay a contractor, but nothing more.

SurePayroll: Best for alerts

App Store rating: 4.8 stars (2.6K reviews)⁷
Google Play rating: 4 stars (40 reviews)⁸

SurePayroll is owned by Paychex, our top pick—which goes to show that Paychex’s team is absolutely committed to making user-friendly, accessible apps. With the SurePayroll app, you can record your employees’ hours worked as well as their vacation days, sick leave, and other PTO accruals. Access customer service right from your phone or tablet, pull up payroll reports on individual employee earnings and tax deductions, and pay both W-2 employees and 1099 contractors.

SurePayroll also proactively addresses some of the key concerns users have with payroll apps—namely accuracy and security:

• After you enter hourly or contractor hours on your phone, you can see a preview of your payroll before submitting it to make sure you recorded the information correctly.
• The app logs you out after a period of inactivity to protect employee information and company data.
• SurePayroll protects your data with industry-leading encryption and never sends account information via the app.

Want a little extra help staying on top of payroll? SurePayroll sends mobile alerts that let you know when your payroll has been submitted and approved. You can also see compliance changes and payroll deadlines with the app.

SurePayroll’s plans and pricing have changed a lot recently, undergoing at least three major changes in the last six months, so we can’t say for sure these plans will stay the same for long. For now, though, SurePayroll offers two affordable plans: a self-service plan and a full-service plan.

Even though you’ll e-file taxes yourself if you choose the self-service plan, SurePayroll promises to accurately calculate payroll taxes for easier filing. The company even backs up its accuracy with what it calls a Tax Accuracy Guarantee, a perk you won’t see with many other self-service payroll providers.

You won’t see the pricing right up front on the site—instead, you have to offer your name, phone number, and email address to generate payroll plan and pricing information. It’s not completely transparent, but it’s certainly better than having to trade all your information to a sales agent for a quote.

QuickBooks Online Payroll: Best accounting integration

App Store rating: 4.2 stars (844 reviews)⁹
Google Play rating: 3.4 stars (1.5K reviews)¹⁰

QuickBooks’ payroll app is a little less robust than the others we’ve reviewed so far. But that doesn’t mean it skimps on standout on-the-go payroll features:

• Payroll runs
• Payroll reminders
• Free direct deposit
• Bank-grade security
• Past paychecks access
• Tax e-filing

That’s right—you can file taxes, pull up tax forms, and see tax payments using the QuickBooks Online Payroll app, which isn’t something you can do with every payroll application.

What QuickBooks Payroll lacks in features, though, it makes up for in integration—that is, easy integration with QuickBooks Online, one of the world’s most popular accounting programs. When you sync QuickBooks Payroll with QuickBooks Online, your books automatically update and you gain access to dozens of customized reports that let you know where your business is going (and how payroll figures into those numbers).

Until recently, QuickBooks offered only two payroll plans: self service and full service. The self-service plan started at $45 per month and didn’t include automatic payroll filing, which was, frankly, ridiculous at that price. Luckily, QuickBooks has rectified the error; now, it offers only full-service plans, which means Core, Premium, and Elite all include automatic tax filing.

Still, $45 a month is a bit steep for basic payroll. Gusto, our top pick for small-business payroll software, starts at $39 per month; Square and SurePayroll both start at under $30. And only the Elite plan comes with a tax-filing guarantee, meaning QuickBooks pays any penalties associated with tax errors (most other payroll companies offer a tax-filing guarantee with all their plans, not just the most expensive ones).

QuickBooks’ new-and-improved payroll plans have some definite perks, though. The Core plan includes an automatic payroll option, health benefit access, and next-day direct deposit. Who knows—with these new changes, QuickBooks’ payroll app’s figures could change as well, hopefully for the better. (We’ll keep our eye on the situation and update accordingly.)

RUN Powered by ADP: Best for HR

App Store rating: 2.4 stars (162 reviews)¹¹
Google Play rating: 2.5 stars (1.7K reviews)¹²

ADP is best known as a PEO, or professional employment organization. But ADP offers software too—including payroll and HR software in the form of RUN Powered by ADP. Along with all the basic payroll features, the app includes some helpful HR services:

• Access to employees’ contact information and pay rates
• HR tips and alerts
• HR document access
• Report sharing

We know those bullet points are a little vague . . . and that’s because the app description itself is vague. As per both the App Store and Google Play, you can “view, filter, print, and share easy-to-read reports” with RUN, but the description doesn’t list what kinds of reports you can see.

The RUN app also has a lot more customer complaints and bad reviews than any other apps we reviewed here. Apparently the app doesn’t work well (or at all) overseas, and it definitely can’t do everything the software can do.

Still, we’re glad RUN has an app: most payroll software doesn’t. And we like that you get at least a few HR features with every plan, even the most basic one.

Like we said above, no matter which RUN plan you choose, you get at least a few basic HR features—which makes RUN Powered by ADP best suited for small businesses on the slightly larger end of small (say, 20 or more employees).

Plus, RUN doesn’t list its plans’ costs online. Sure, the app’s low star rating is a major strike against it, but so is the company’s lack of transparent pricing. After all, QuickBooks is expensive, but at least the company isn’t afraid to list its pricing.

Gusto and Patriot Software: App-free internet access

Using an app is often the most convenient way to run payroll on the go—but it isn’t the only way. In fact, a company can optimize their software to work just as well on a full-width laptop screen as on a small mobile screen.

Why stick to a browser instead of creating an app? For one thing, some of the apps we listed above don’t have the same features as their full-fledged software counterparts. But if your payroll company has optimized their site for mobile, you just open your preferred internet browser’s app, type in your payroll software company’s web address, and have exactly the same software experience on your phone as you would on a desktop.

This is the tack one of our favorite payroll software companies, Gusto, has decided to take. So has another of our most affordable picks, Patriot Software.

Gusto: Most comprehensive plans

Gusto offers three plans: Core, Complete, and Concierge. Each full-service payroll plan includes health benefit add-ons, workers compensation administration, and PTO policy creation. At $39 a month with a $5 additional fee per employee, it’s reasonably priced (more so than QuickBooks), and like we said above, you can access all of Gusto’s features online on your mobile device, app-free.

Patriot Software: Most affordable self service

Patriot’s plans are cheaper than Gusto’s at $30 a month for full-service payroll with a $4 add-on cost per employee. It also offers a self-service plan, meaning a plan without automatic payroll tax filing, at just $10 a month with the same per employee cost. If you have only a handful of employees and aren’t too stressed about taxes, Patriot’s reliable self-service software could be a good choice. Both the self- and full-service plans include free direct deposit, employee self-service payroll portals, workers compensation integration, and unlimited payroll runs.

FAQs

Are payroll apps free?

The apps listed here are free with the purchase of the associated software. For example, Paychex Flex’s app is included at no additional cost with your Paychex Flex payroll subscription.

None of the payroll software we listed here is free, but you can hop over to our piece on the best free payroll software to learn more.

The takeaway

The online payroll services listed here are way ahead of the curve in making payroll management as easy, accessible, and convenient as possible—and their apps have the features to prove it. Whether you’re on the road heading to your next farmers market, or taxiing on the runway before your next business trip, these cloud-based solutions give you the flexibility to pay your employees on time, every time.

Looking for more than payroll software? Check out our favorite cloud-based accounting software for small businesses—most of which pair easily with your preferred payroll solution.

Disclaimer

At Business.org, our research is meant to offer general product and service recommendations. We don’t guarantee that our suggestions will work best for each individual or business, so consider your unique needs when choosing products and services.

Sources

1. Statista, “Share of Global Mobile Website Traffic 2015-2019”
2. Statista, “Share of Global Mobile Website Traffic 2015-2019”
3. App Store, “Paychex Flex”
4. Google Play, “Paychex Flex”
5. App Store, “Square Payroll”
6. Google Play, “Square Payroll”
7. App Store, “SurePayroll for Employers”
8. Google Play, “SurePayroll for Employers”
9. App Store, “QuickBooks Payroll”
10. Google Play, “QuickBooks Payroll for Employers”
11. App Store, “RUN Powered by ADP”
12. Google Play, “RUN Powered by ADP Mobile Payroll for Employers”