Pick the best payroll app for your business – The Top Ten

We check out ten of the best to deal with payroll.
23 June 2022

The right payroll app can save your business time, money, and frustration.

We round up the best payroll app for your business – whatever it looks like.

Payroll apps are not by any means just payroll apps. They’re the Swiss Army knife of apps that help any business, whatever its size, pay its staff on time, organize its HR function, track time, and even retain staff that might otherwise leave.

But payroll apps often overlook what you really need, while making you pay for functionality you’ll never look at again. Picking the right payroll app for your business can save you worlds of frustration and time. But how do you know which is the right one for you?

You’ll know because of all the things you can’t do right now. That’s the starting point to tell you your current payroll solution is not optimized for your business. The things you can’t do, that would make your life easier if you could.

In very broad strokes, it’s true to say that an SME will have different requirements from a payroll app than a larger enterprise. So first of all, know which your business is. Size is not all-important, but it identifies the kind of things you’re most likely to need from a payroll app at your level, and makes some apps more useful to you than others.

Best Payroll Apps for SMEs

If you work in an SME, one of the main benefits of a payroll app is the sheer amount of work you can get done straight from the app. Another is how simple and accessible the app makes it to of what you need, and get on with your day. On those two key criteria, there are five front-runners in the market today.

QuickBooks Payroll

Quickbooks Payroll benefits from a high level of market recognition, but that’s not what puts it at the top of our list of payroll apps for SMEs. What does that is the amount that QuickBooks Payroll lets you do from your phone or tablet. You can run your payroll, obviously. But you can also make same-day or next-day deposits, pay both employees and contractors from the same app, and even e-file your taxes. That checks a lot of SME boxes, right out of the gate.

Allied to that level of functionality, there’s the fact that a lot of SMEs use QuickBooks for their main accounting software. QuickBooks Payroll syncs easily with the full-scale product, so it’s a connected experience that doesn’t leave gaps for important payroll data to fall through. It’s also relatively easy to learn and use, inspiring confidence at first, and taking a lot of the pain out of the payroll process as you use it more. And being a well-recognized brand means QuickBooks can’t afford to develop a reputation for poor customer service, so you have access to expert support whenever you need it with the app.

That’s what makes QuickBooks Payroll a wise choice for a lot of SMEs.


If you’re a one-person business, or you’re growing fast and need some flexibility in your payroll app, Paychex is definitely worth a look for your business. While you can’t run an unlimited number of pay runs, you can review and approve PTO requests from the app. Quickbooks Payroll won’t let you do that.

The limited number of pay runs is what makes Paychex more suited to small and growing businesses. The freedom to approve PTO (paid time off) requests is a useful add-on at that scale. It’s also worth noting that with Paychex, you have several options for ways to pay. You can use paper checks, direct deposits, pay-on-demand, and more.

What elevates Paychex though is its flexible pricing structure. If you’re a solopreneur, there’s a plan especially for you. In fact, there are three levels of pricing. That means you never pay for more features or functionality than your business needs.

Square Payroll

Square Payroll is a favorite payroll app of the hospitality industry and retail stores, because it pairs with the Square POS. But it’s by no means only for those sectors. Any business model where you need rapid employee payments fits into the wheelhouse of Square Payroll.

Like QuickBooks Payroll, you can’t review or approve PTO requests from the app, but you can use Square Payroll to get both long-term staff and even hourly contractors paid with a couple of taps and a swipe.

There’s some flexibility on pricing with Square Payroll, and it’s particularly attractive if you only pay contractors.

What pushes Square Payroll down the list of the best payroll apps though is some unhelpful clunkiness. You need a Square Payment account if you want to make next-day deposits, for instance. And the app is only available to employers – employees wanting to check their pay need to download a different app.


If you need a payroll app that’s relatively no-fuss and does a little of everything, it’s worth considering Fingercheck. Combining payroll, HR, and some time tracking functions in one, Fingercheck gives you the best of both worlds. It will let you make unlimited pay runs, like Quickbooks Payroll, and review and approve PTO requests, like Paychex.

It also brings a trick or two of its own to the table, including payroll financing – frequently needed by early-stage start-ups – and a dedicated portal for accountants. It’s priced competitively, but one of the things that drags it down the list is the cost of optional add-ons, like time-clock software, an automated clearing house, and even an HR concierge. While none of those are essentials for a start-up, the system is built so you’ll notice that you don’t have them pretty fast. Added to that, Fingercheck does not play especially well with third-party software, and adding new staff to the system can be more painful than you’d like.

But, if you want a fully-featured app that does all the things Quickbooks can do for less, Fingercheck is worth taking a look at before you make your final decision.


If cashflow is tight in your early days and you have some technical skills to fall back on, SurePayroll is an attractive option. Owned by Paychex, it’s fairly fully-featured and lets you manage a lot of HR work from the app, as well as processing your payroll. Sick leave, vacation days, Workers Comp, and other PTO requests can all be dealt with from a fairly sturdy and reliable app. And the data security on SurePayroll is impressive, too.

The basic SurePayroll app is available for significantly less than, say, the basic QuickBooks Payroll package. So, if you’re setting up and starting out with tight budget restrictions, SurePayroll can give you a viable option for your payroll and HR management without becoming an economic liability in its own right.

Payroll Apps for larger enterprises

If you’re working in or running a larger enterprise, your payroll app needs to be able to handle a lot more data, and to do a lot more with the data it has. That’s why usually, the best payroll apps for this size of business are a league apart from those that work perfectly well for SMEs.


Cintra thrives on the flexibility of its offering. If you have the money, you can simply pay Cintra as a fully outsourced payroll operation, and get on with the business of expansion.

But it also has a range of other packages at levels to suit you, from Cintra Serve, a supported self-serve package where you do most of the work, to Cintra Consult, where the company acts as your payroll and HR consultant. Cintra SaaS is probably the most widely used option in large enterprises, though, as the app fully integrates your payroll and HR functions into a single source, and gives you both flexibility, data security, and the power to manage all the day-to-day processes of payroll and HR from the app.

The support offering with Cintra stops short of a chat facility, but borrows from Apple in terms of having a knowledge bank and FAQ resource alongside email and phone support. There are also a wide range of training options with Cintra, from the traditional in person option to the Covid-era option of live online training.

One thing to watch out for with Cintra though is that – unlike several other apps – it doesn’t offer 401(k) tracking, so if that’s crucial on your payroll app wish list, you’d best look elsewhere.


Rippling has gained a strong reputation as a payroll app by combining a lot of functionality into a single portal, and then making it relatively simple to use. If you want it to, the Rippling app can manage all your payroll, HR, benefits and IT needs, making it a multifunctional tool for your enterprise. Usually, when you put too many eggs in a single basket, something gets forgotten or overlooked, but Rippling covers a lot of the necessary waterfront for you by automating a lot of its processes. It’s fast and easy when it comes to onboarding new staff, and it plays well with third-part software, too, so if you need that level of flexibility, it’s an impressive option to investigate.

One point of caution with Rippling – which could also be among its benefits – is that it’s priced for smaller businesses, with a modular structure that lets you add the features you need, rather than paying for unnecessary extras that sit and do nothing for your enterprise. The support option with Rippling is more extensive than that offered by Cintra, in that it includes a chat support function alongside the standard phone and email, but also doesn’t skimp on the knowledge base and FAQ section.

Training is more wholly 21st century though, with webinars and live online training very much to the fore, and no in person training option, so if you need that “in the room” training model, go with Cintra rather than Rippling. Then again, if you need 401(k) tracking, Rippling will satisfy you more than the Cintra offering.


Relatively new in the market but growing exponentially and with an impressive client base including Intel, Toyota, Wix, and Johnson & Johnson, PapayaGlobal is more of a fully-functioning management tool than strictly a payroll app. That said, it does everything you expect it to do as a payroll app, it just has the muscle to do much more if you need it to.

The particular niche in which PapayaGlobal operates best is the multinational company, because it acts as a smooth cross-border payroll app, so you get none of the usual headaches that entails.

There are several service levels with PapayaGlobal, including a simple payroll management level and a payroll intelligence suite. If you need a full-on payroll and employee management system that works effortlessly across several countries, PapayaGlobal is worth your time and interest. But beware – if that’s not what you need, you can find a better fit on a smaller scale, and spend less of your enterprise’s money.


BambooHR is a Hail Mary inclusion on the list of the best payroll apps for large enterprises. That’s because as the name suggests, it’s an HR-focused app first and foremost. But there’s a surprising level of in-depth payroll functionality embedded in the app too, and it’s very straightforward to operate.

Payroll management and payroll reporting are simple functions in the app, which also includes employee onboarding and management within its more HR-focused capabilities. BambooHR works well for enterprises operating in multiple countries, and is available in up to 6 languages, which can make it attractive to multinational operations.

Where BambooHR falters compared to some of the purely payroll options is that, for instance, it has no ability to deliver attendance tracking or management, so if you want that kind of data, an app like Cintra or Rippling is more suited to your needs.


In the Covid era, more large enterprises found that their employees were more dispersed. Remote delivers payroll and HR functions to large enterprises with increasingly remote-first workforces.

Remote has four pricing plans, depending on the nature of your needs. You can choose the Contractors plan if you’re dealing mostly with workers on contracts. But there’s also a simple Payroll & Benefits plan, and a Global Employment plan, depending on the size and scope of your enterprise.

International remote payroll is where the Remote app lives and breathes. In fact, the company was founded in 2019 specifically with remote workforces in mind. That makes it suitable for enterprises that are distinctly remote-first. If you have less than 50% of your workforce operating remotely, you’d be better served by the likes of Cintra or Rippling. But with remote work becoming a dominant trend in the post-pandemic world, Remote is worth looking at, either now or for the future.


When you’re choosing the right payroll app for your business, work out exactly what you need, and what you don’t. There are apps to suit almost every business profile. Knowing what you can’t do without will serve you better than  going with the most popular option.