Square vs. QuickBooks Payroll Comparison 2022

These companies are best-known for other software. Here's how their payroll products stack up against each other.
Nina Godlewski
By Nina Godlewski 
Edited by Rick VanderKnyff

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If you’re looking to streamline your payroll processes, finding the right software is key. However, with so many available options, it can be difficult to choose the best one for your business. This guide provides a detailed comparison of Square vs. QuickBooks payroll solutions to help make your decision easier.

Square vs. QuickBooks Payroll: Overview

When it comes down to it, the right payroll software for your business will be the one that provides the features you need at a price point that fits your budget. You’ll also want to consider things like usability and integrations, or how it will work in conjunction with your other business management software platforms.

When it comes to Square vs. Intuit payroll, both are cloud-based systems, meaning you can access them from any device with an internet connection. You can expect a full range of payroll distribution and tax functionality, as well as additional features in each.

If you use another Intuit or Square product already (say, QuickBooks Online accounting software or Square’s POS system), it will likely be a clear choice which platform is better suited for your business. After all, being able to sync multiple business platforms will help you more easily manage your business finances. However, if you don’t already use a Square of QuickBooks product, you’ll have to consider more factors before making a decision.

Here’s a high-level look at how Square Payroll vs. QuickBooks compare.

Square Payroll vs. QuickBooks Payroll

Square Payroll

Shop Now

on Square's website

QuickBooks Payroll

NerdWallet rating 
Shop Now

on QuickBooks' website


Payroll, Payroll for Contractors

Core, Premium, Elite


$35 per month + $5 per employee per month (no monthly if you’re only paying contractors)

$45, $75, $125 per month


Employer resources, automated tax filing, benefit management

Tax protection, personal HR advice, custom setup

Free trial


30 days

Square Payroll plans and pricing

One of the best things about Square Payroll is that if you only pay independent contractors each month, you have a very affordable option because you get to skip the monthly per-employee fee. However, their payroll software serves more than just contractors. Here are the details of Square Payroll for both full-time employees and contractors.

Square Payroll

The standard Square Payroll plan costs a base price of $35 per month and then an additional $5 per employee per month that you pay using their system. This service comes with all of the features you would need to run your payroll.

  • Payroll: With Square Payroll, you can create your own payroll schedule for direct deposit and pay your hourly and salaried employees on a weekly, bi-weekly, semi-monthly or monthly basis. Not only can you handle payroll, but you can also designate any deductions for 401(k) contributions, taxes and more.

  • Automated tax filings: Square Payroll will also handle a ton for you in the way of payroll taxes and tax filing. It can handle your tax withholding and payments so when you run payroll, the taxes are already calculated and sent off to the state and federal agencies. The system will also file your tax forms on a quarterly basis and at the end of the year. The forms for the IRS and the social security administration will also be done and filed for you.

  • Time-saving tools: All of the services Square Payroll is offering are time-saving tools, but you can save even more time by importing employee hours from the Square point of sale app (if you also use this app). Other time-saving tools include employee invitations for easy setup and the option to have employees clock in and out at the register.

  • Employee benefits: You’ll be able to sort through your employee benefits and manage them from within Square Payroll. Benefits like health, dental and vision insurance and more can all be selected and then administered to employees. The platform can also support workers compensation insurance, 401(k) and retirement savings, pre-tax benefits, like commuter benefits and more. You choose the benefits plan, invite your team to sign up and Square Payroll will handle the deductions as necessary.

  • Employer resources: The employer resources center of Square Payroll helps you do everything from hiring new employees to applying for an employer identification number.

Square Payroll for contractors

In addition to Square Payroll, there’s a specific product for business owners who only need to pay contractors each month. This service can be combined with the standard Square Payroll plan (i.e. if you employ both full-time employees and contractors) or it can be used independently (if you only work with contractors). When used independently, it costs $5 per contractor you pay each month, but there is no monthly fee.

  • Form 1099-MISC: If you use Square Payroll for Contractors you’ll find that your Form 1099-MISC is filed for you. All of the information from your contractors is taken care of by Square: They prepare the form and file it online for you so you have all of the information you might need about your contractors whenever you need it. Your contractors will also be able to download this form from their accounts when they need to do their taxes.

  • Direct deposit: As with salaried employees, you can also allow your contractors to set up direct deposit so they can receive payment more easily and you can quickly track payments. Contractors, on the other hand, can also receive notifications when payment is received.

  • Time tracking: You can also seamlessly import timecards from the Square Point of Sale app or one of their other timecard partners, so you don’t have to manually import hours each week. This can make time-tracking easy and accurate for your business and for your contractors. Plus, Square can also help you calculate and pay out credit card tips processed by Square in just one click.

QuickBooks Payroll plans and pricing

With QuickBooks Payroll, you have the option to choose from three different plans for your payroll needs: Core, Premium and Elite. As each plan increases in price, you’ll also get more features, which are detailed below.

QuickBooks Payroll Core

For $45 per month and then an additional $4 per employee per month, you can get the payroll essentials with this full-service payroll software. Like Square Payroll, you will also receive tax help and additional functionality.

The features you get with QuickBooks Payroll Core are:

  • Full-service auto payroll

  • Manage health benefits

  • Expert product support

  • Next-day direct deposit

  • Fast, unlimited payroll runs

  • Paycheck and tax calculation

  • Automated tax filing

  • Workforce portal

  • Payroll reports.

QuickBooks Payroll Premium

The QuickBooks Payroll premium plan comes with all of the features included in the Core plan, plus even more.

The Premium plan costs $75 per month and then an additional $8 per employee per month. In addition to everything included in the Core plan, you’ll also have:

  • Same-day direct deposit

  • HR support center

  • Expert setup review

  • Time tracking on the go.

If you’re worried about setting up payroll on your own and don’t have a dedicated HR team on staff, the expert setup review may be especially helpful.

QuickBooks Payroll Elite

The third and final plan offered by QuickBooks Payroll is the Elite plan at $125 per month plus $10 per employee per month. Again, you’ll have access to all of the features in QuickBooks’ first two plans, plus even more.

The features that come with Elite include:

  • White-glove setup

  • 24/7 expert product support

  • Time and project tracking on the go

  • Tax penalty protection

  • Personal HR advisor

  • Workers compensation administration.

As you can see, this plan has the most comprehensive feature-set. You’ll have full-service support to help you set up and manage your payroll and tax needs, as well as an HR advisor to answer any of your day-to-day questions. Plus, with tax penalty protection, you can rest assured that if your business is issued any fees or penalties for filing handled by QuickBooks, they’ll cover it.

Square Payroll pros and cons

As you decide whether Square Payroll or QuickBooks payroll is best for your business, it’s helpful to look at where each product stands out, as well as where it falls short.

Square Payroll pros

  • Pricing: It’s a huge plus that Square can be used specifically for paying contractors if you need to. The fact that it’s just $5 per contractor per month can be great for businesses that only employ contractors. Even if you employ both contractors and salaried employees (or only salaried employees), Square Payroll still costs less overall than QuickBooks Payroll, making it a great option for small businesses on a budget.

  • Tip tracking: Another pro for Square Payroll is the fact that you can easily import hours worked and tips earned from the Square POS app, meaning you save significant time you would otherwise have to spend manually importing this data. Again, this is a major pro for service-based businesses with hourly employees.

  • Ease of use: One of the things Square users highlight is its ease of use, making it ideal for new business owners who are using payroll software for the first time and don’t have a ton of time to devote to the system. “I use Square for a side business, and I love its simplicity. The setup and execution was very straightforward,” John Holloway, co-founder of NoExam.com, explains.

Square Payroll cons

  • Customer service: Some users have reported that they found it difficult to get in touch with the customer support services for Square Payroll. While Square has a telephone number along with live chat and online resources, some users still find it difficult to get the answers they need.

  • Reliance on Square products: While Square supports integrations with other apps and tools, you’ll find it easiest to use and take full advantage of Square Payroll’s capabilities if you use Square POS as well. If you’re already a member of the Square family, this can be a pro for the system; however, if you use other platforms, this may not be your first choice.

QuickBooks Payroll pros and cons

Now, it’s time to see how QuickBooks stacks up. Here are some big advantages and disadvantages to consider.

QuickBooks Payroll pros

  • Tax help: QuickBooks Payroll will handle your payroll taxes and if you opt for the Elite plan, you also get the tax penalty protection of up to $25,000 per year. So, not only will QuickBooks Payroll manage and file your payroll taxes (which Square also does), but they take it one step further with the tax penalty protection. Again, you’ll have to opt for the highest-level plan for this protection, though.

  • Integration with QuickBooks: While QuickBooks Payroll doesn’t integrate well with other third-party tools or apps, it does work well with other QuickBooks products. If you use QuickBooks for your accounting or you use QuickBooks Online, it will work seamlessly with this payroll software. This can help you seamlessly import information between apps and save time all around.

QuickBooks Payroll cons

  • Lack of integrations: If you don’t use QuickBooks for your other business needs, using their payroll product might actually make more work for you than it’s worth. It does not integrate with any third-party tools or apps, so you’ll have to manually move a lot of information around, which could lead to more errors on your end. Plus, unless you opt for the more expensive plans, you won’t have access to HR resources or have to option to connect them with a third-party system.

  • Pricing: Compared to Square, QuickBooks Payroll is a significantly more expensive option, especially considering that you can’t connect it to other tools you use to manage your business.

A version of this article was first published on Fundera, a subsidiary of NerdWallet

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