The 5 Best Payroll Apps for Small Business 2021

Just a few payroll software companies have employer-facing payroll apps, so if mobile payroll is a must for you, these five providers—including Paychex and QuickBooks—are your main options. All five of these apps have solid features and user reviews, so no matter which company you choose, you should have a good mobile experience.
Best overall
Paychex
Paychex Flex
  • Icon Pros  Dark
    Comprehensive employer- and employee-facing apps
  • Icon Pros  Dark
    HR administration
Most affordable
Square
Square
  • Icon Pros  Dark
    Easy syncing with Square Point of Sale
  • Icon Pros  Dark
    Contractor-only plans with no monthly base fee
Best for alerts
SurePayroll
SurePayroll
  • Icon Pros  Dark
    Mobile payroll alerts
  • Icon Pros  Dark
    Industry-leading data encryption
Best for HR
ADP
RUN Powered by ADP
  • Icon Pros  Dark
    Easy remote employee management
  • Icon Pros  Dark
    HR document access and sharing
Best integration
Quickbooks
QuickBooks Online Payroll
  • Icon Pros  Dark
    Simple integration with QuickBooks Online accounting software
  • Icon Pros  Dark
    Mobile tax e-filing

While most payroll service providers offer mobile apps for employees, software lags on the small-business employer side. Only a handful of payroll software companies have employer-focused apps for small-business owners who value paying employees anywhere, anytime. Luckily, the few brands that do offer employer-facing payroll apps have put in the time, energy, and labor to make absolutely stellar products. Here are our picks for the best small-business payroll apps of 2021.

The best payroll apps for small business in 2021

Best payroll apps plans and pricing

Payroll provider
iOS or Android
Payroll type
Starting base price
Additional cost per employee
Learn more
Paychex Flex

Both

Full service

$59.99

$4.00/payee

Square Payroll

Both

Full service

$29.00/mo.

$5.00/payee

SurePayroll

Both

Self service and full service

$19.99/mo.

$5.00/payee

RUN Powered by ADP

Both

Full service

Contact for quote

Contact for quote

QuickBooks Online Payroll

Both

Full service

$45.00/mo.

$4.00/payee

Data effective 12/3/20. At publishing time, pricing and features are current but are subject to change. Offers may not be available in all areas.

Paychex Flex: Best overall

App Store rating: 4.8 stars (199.5K reviews)1
Google Play rating: 4.5 stars (16.1K reviews)2

Paychex

Paychex Flex’s plans aren’t the cheapest, but its payroll app is easily the best one out there. If running payroll from anywhere in the world on any web-enabled device is a must for you, Paychex Flex is the way to go.

Paychex Flex’s app is far and away the most popular payroll app for small businesses. So what makes it so great? For one thing, it does basically everything Paychex's stellar cloud-based payroll software can do—and it does quite a lot. Paychex's plans include standout HR support, including dedicated HR specialists with pricier plans. Accessing all that info on the go on a fantastic app that nixes bugs and app crashes is a bargain.

Speaking of bug- and crash-free apps, Paychex's 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 make a meeting, you can pick up right where you left off on your phone after you're through. 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.

Pros
Pro Bullet Fantastic mobile app for employers and employees
Pro Bullet Robust plans featuring dedicated HR solutions
Pro Bullet Three full-service plans starting at $59/mo.
Cons
Con Bullet Pricer plans than many competitors
Con Bullet Extra fee for accounting software integration and multiple employee pay options

Square Payroll: Most affordable

App Store rating: 4.8 stars (3K reviews)3
Google Play rating: 4.4 stars (493 reviews)4

Square

If you work primarily with contractors, don’t want to pay extra for running payroll as many times as you need during the month, and need a super intuitive app, Square Payroll is the best (and most affordable) payroll option for you.

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.

Finally, along with running payroll, you can use Square’s app to track employees’ paid time off (PTO), sick leave, and overtime. That's not bad for a straightforward, completely affordable app.

Best Small Business Payroll Software
Gusto
Best overall
ADP
Best HR add-ons
Paychex
Best reporting
OnPay
Simplest setup
SurePayroll
Best customer service
Learn more about our top brands.
Pros
Pro Bullet Syncs easily with other popular Square products, including Square Point of Sale
Pro Bullet No monthly base fee for contractor-only plan
Pro Bullet Intuitive, user-friendly app
Cons
Con Bullet Less scalable than competitors like Paychex and ADP
Con Bullet Fewer reports than competitors

SurePayroll: Best notifications

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

SurePayroll

SurePayroll’s mobile alerts, customer service access, and detailed reporting keep you on top of on-the-go payroll.

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. Most importantly, it 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.

Pros
Pro Bullet Affordable pricing starting at $19.99/mo.
Pro Bullet Solid mobile app with excellent security and notifications
Pro Bullet Workers compensation and health insurance add-ons
Cons
Con Bullet Less impressive Android app
Con Bullet Extra fee for two-day payroll processing and accounting software integration
Tired of payroll? Gusto handles payroll taxes and more

With unlimited payroll runs and automatic tax filing, Gusto helps small-business owners worry less about payroll and put more time into growing their business.

  • Get automatic payroll tax filing, including end-of-year tax forms
  • Manage workers compensation insurance
  • Track paid time off, sick leave, and holiday pay

RUN Powered by ADP: Best HR

App Store rating: 2.2 stars (249 reviews)7
Google Play rating: 2.6 stars (1.8K reviews)8

ADP

If you need HR solutions alongside mobile payroll, RUN Powered by ADP puts HR management tips, compliance assistance, and new-hire onboarding at your fingertips.

We know you're looking at those user reviews and thinking, this app? Really? But hear us out: while ADP's app isn't the strongest, its software is one of our absolute favorites. Like Paychex, ADP offers a slew of HR features, which makes it a great fit for midsize and large businesses. With multiple plans and price points, it's also a scalable choice for businesses planning on growth.

But the app? Well, the app leaves a little to be desired. Customers report problems with forced logouts, and many are frustrated with the app's lack of features—for the most part, it works for payroll runs only and doesn't offer the support of ADP's software.

Still, the app does offer some payroll features alongside its HR assistance:

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

We know that's vague, but bear in mind that ADP is still one of the few payroll providers to even have an employer-facing app. And we've got our fingers crossed that they bring the app up to par with the software sooner than later.

Pros
Pro Bullet Comprehensive plans with thorough HR features
Pro Bullet Time and attendance integration
Pro Bullet Versatile plans to accommodate small businesses (1 employee) to big businesses (1,000+ employees)
Cons
Con Bullet Poorly reviewed app
Con Bullet Expensive plans with no transparent pricing on site
Con Bullet Poor customer reviews

QuickBooks Payroll: Most user-friendly

App Store rating: 4.3 stars (1.1 reviews)9
Google Play rating: 4.2 stars (1.7K reviews)10

Quickbooks

Already using QuickBooks Online? QuickBooks’ payroll app syncs easily with your existing accounting software, making bookkeeping a breeze.

QuickBooks’ payroll app is a little less robust than the others we’ve reviewed so far. But that doesn’t mean it skimps on features: you can use the app for payroll runs and reminders, direct deposit, bank-grade security, and even e-filing your taxes.

Like QuickBooks Online's accounting app, its payroll app has a low learning curve. With a sleek dashboard and few glitches, we'd say it's the most user friendly of all our app options listed here. In fact, QuickBooks Payroll's app is much better than ADP's—so why'd we give it a lower rating?

Unfortunately, while QuickBooks Payroll's app is great, the software itself isn't. It's pricier than similar providers without adding more features, but most importantly, QuickBooks Payroll only includes an industry standard tax filing guarantee with its most expensive plan. Without that guarantee, you're on the hook for any payroll errors QuickBooks makes when it files your taxes for you—and yes, that's as ridiculous as it sounds. So while we like the app, we can't recommend QuickBooks' payroll solution over ADP's.

Pros
Pro Bullet Syncs flawlessly with QuickBooks Online
Pro Bullet User-friendly app with low learning curve
Pro Bullet On-the-go tax e-filing
Cons
Con Bullet Tax filing guarantee with most expensive plan only
Con Bullet Fewer mobile features than competitors

Mobile-friendly honorable mentions

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 its software to work just as well on a full-width laptop screen as on a small mobile screen, and that's just what Gusto and Patriot Software—two of our favorite payroll providers—have done.

Gusto: Most comprehensive plans

Gusto

Gusto’s affordable plans include workers compensation insurance and health benefits administration. As long as you’re comfortable using an internet browser app to access payroll, it’s hard to do better than Gusto.

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 Software Logo

Don’t mind dealing with taxes yourself? Patriot Software’s $10-a-month plan still includes key features like workers comp integration and unlimited payroll processing.

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.

Payroll app FAQ

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. App Store, “Paychex Flex.” Accessed December 4, 2020.
2. Google Play, “Paychex Flex.” Accessed December 4, 2020.
3. App Store, “Square Payroll.” Accessed December 4, 2020.
4. Google Play, “Square Payroll.” Accessed December 4, 2020.
5. App Store, “SurePayroll for Employers.” Accessed December 4, 2020.
6. Google Play, “SurePayroll for Employers.” Accessed December 4, 2020.
7. App Store, “RUN Powered by ADP.” Accessed December 4, 2020.
8. Google Play, “RUN Powered by ADP Mobile Payroll for Employers.” Accessed December 4, 2020.
9. App Store, “QuickBooks Payroll.” Accessed December 4, 2020.
10. Google Play, “QuickBooks Payroll for Employers.” Accessed December 4, 2020.

Kylie McQuarrie
Written by
Kylie McQuarrie
Kylie spent two of the last four years writing for and with small-business owners—from dentists in Australia to plumbers in the Midwest. She spent the other two writing in depth about internet and security. She’s passionate about reading, hiking, and dedicating every spare second to writing for fun (at lunch, between meetings, on the train, before breakfast . . . ). Her content helps small-business owners tackle the logistics of running a business so they can focus more on their passions too.
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