Square Payroll vs QuickBooks Payroll: Which Is Best & Why
Charlette has over 10 years of experience in accounting and finance and 2 years of partnering with HR leaders on freelance projects. She uses this extensive experience to answer your questions about payroll.
This article is part of a larger series on Payroll Services.
Square Payroll and QuickBooks Payroll are both a great fit for small businesses; they run full-service payroll (files and pays your payroll taxes), offer benefits like health insurance and retirement, and are widely used. Square Payroll is cheaper—especially if you’re only paying contractors– but is limited in reporting capability. It’s also ideal if you’re using Square POS. QuickBooks Payroll syncs seamlessly with QuickBooks accounting software and is great if you need to pay employees quickly.
Here’s when we particularly recommend Square Payroll or QuickBooks Payroll:
- Square Payroll: Best for retail, restaurant, or appointment-based businesses that want affordable but easy-to-use payroll software with some HR benefits. Especially good for Square POS users.
- QuickBooks Payroll: Best for service and other businesses, especially those already using QuickBooks Accounting.
There are times when neither Square nor QuickBooks is the best payroll solution. In general, the best alternative to Square vs QuickBooks for payroll is:
- Rippling: Best payroll service for companies with remote employees or a global workforce.
Square Payroll vs QuickBooks Payroll Compared
 |  | |
Monthly Pricing | $35 + $5 per employee, contractor-only plan: $5 per contractor | $45–$125 + $4–$10 per employee |
Payroll tax filings and year-end reporting | Federal, state, local | Federal and state; local with higher plans |
Time tracking | ||
Direct Deposit processing times | 4 days or instant with Square Instant | Next-day |
Health insurance, retirement, workers’ comp | ||
Low-cost contractor-only plan | No | |
State New Hire reporting | Report generated | |
Employee onboarding | ||
Access to payroll specialists | ||
Access to HR advisers | - | |
Integrations | Square systems | Hundreds through QuickBooks Accounting |
If you are looking for an alternative that is richer in HR features, check out our list of best payroll solutions.
When to Choose Square Payroll
Square Payroll is the superior choice for retailers, restaurants, and appointment-based businesses because of its excellent POS system. If you use Square POS, then Payroll integrates seamlessly, making paying your employees and contractors a breeze. However, you can use Square Payroll without a Square POS account.
Even without Square POS, it’s still an excellent choice. It’s highly affordable, covers hourly and salary employees, and handles taxes, commissions, tips, and deductions with ease. Square Payroll is also an excellent choice if you only have contractors, as it has a contractor-only program—QuickBooks does not. This plan handles payroll and 1099s at a far cheaper price.
Square Payroll Pros & Cons
| PROS | CONS |
|---|---|
| Easy to use | HR through third-party app (extra fees) |
| Tax penalty protection | Standard direct deposit takes four days |
| Seamless integration with Square POS | Limited integrations |
| Unlimited pay runs | Need to manually add reimbursements |
| Instant payment through Square Instant Payments | |
| Handles contractors, tips, and more | |
When to Choose QuickBooks Payroll
QuickBooks Payroll, on the other hand, is better for other kinds of businesses, from manufacturing to B2B companies, and it integrates natively with QuickBooks Accounting. It can work for retail, but not as well as Square. Through QuickBooks Accounting, QuickBooks Payroll can pull information from hundreds of other programs, which is a great help if you are paying commissions, mileage, or other payments tracked through third-party software.
QuickBooks Payroll Pros & Cons
| PROS | CONS |
|---|---|
| Choice of pricing plans | Tax penalty protection in Elite Plan only |
| Seamless integration with QuickBooks Accounting | No contractor-only plan |
| Excellent phone app for payroll | Core Plan does not include local tax filings |
| Robust tax penalty protection; QuickBooks to cover up to $25,000/year in tax penalties regardless of who makes the mistake | Basic HR features only |
Most Affordable: Square
Square Payroll is much cheaper than QuickBooks Payroll for two reasons. First, it offers only two cost-effective plans: a contractor and employee plan for $35 per month + $5 per employee, per month, and a contractor-only plan at $5 per contractor, per month. Compare this to QuickBooks at $45 per month + $4 per employee, per month, for its cheapest plan.
Best Payroll & Reporting Features: QuickBooks
While closely matched, QuickBooks beats out Square for payroll features because it offers next-day payroll (same-day with its more expensive plans). Square, meanwhile, takes four days. If you need to track payroll by project, then QuickBooks’ Elite Plan includes project and time tracking, which Square does not.
Both QuickBooks and Square offer a penalty-free guarantee in which they pay associated fines and penalties if their software makes an error. However, with the Elite Plan, QuickBooks will pay your fines regardless of who made the error, up to $25,000 a year.
QuickBooks, however, is far superior to Square when it comes to reporting, with more premade reports as well as greater ability to create specialized reporting. If you are in a highly regulated industry or simply need more data crunching, QuickBooks is the best choice.
Both Square and QuickBooks Payroll have strong payroll features, letting you run payroll automatically and pay employees via checks, direct deposit, or pay card. Either lets you handle salary and hourly employees or contractors and pay commissions and tips. They can handle federal and state taxes, including filing year-end paperwork.
When to Choose Square
Square files local taxes. QuickBooks can calculate local taxes but will only file them in a more premium plan. Square Payroll also lets you pay employees instantly with its Square Instant program. So, if your business accepts customer payments through Square and maintains funds in a Square account, you can pull payroll from your Square account (or associated credit card if you go over the amount in your account) to pay employees quickly—instantly if you have a Cash App account or otherwise, the next day.
If you’re not signed up for the Square Instant Program, payroll takes four days. QuickBooks offers next-day payroll, or same-day with its more expensive plans, regardless of where you store your funds.
Best for HR & Employee Benefits: QuickBooks
QuickBooks squeaks ahead because its Premium and Elite Plans include access to HR support through Mineral. Premium and Elite users can get customizable job descriptions and onboarding and performance tools, and Elite users get personal HR Advisor via phone call as well as assistance with creating policies and handbooks.
Otherwise, Square and QuickBooks are closely matched for HR benefits. Both offer health insurance through SimplyInsured, 401(k) through Guideline, and workers’ comp through AP Intego. Employees can enroll for benefits online through their employee portal. Both have onboarding tools.
When to Choose Square for HR & Employee Benefits
If you need a full-service HR program, Square may be the better choice. It partners with Bambee HR, which provides a dedicated HR specialist for compliance, onboarding and terminations, automated staff training, annual HR audits, and more. Pricing depends on the number of employees and runs $99–$499 per month, plus a one-time audit fee of $0 to $750. The audit fee is at a 50% discount. The HR audit does a deep dive into your HR needs and develops a customized solution with a dedicated manager to get your company up to speed and compliant with regulations.
Best for Integrations: Square Payroll
When it comes to integrations, neither system is very flexible. However, Square Payroll is your better bet. Naturally, it integrates with all of Square’s POS systems, including Square for Retail, Square for Restaurants, and Square Appointments. It also integrates with multiple third-party time trackers that work with Square, whereas QuickBooks integrates with QuickBooks Time. Square also integrates with QuickBooks Accounting, but QuickBooks Payroll does not integrate with Square products.
When to Choose QuickBooks Payroll for Integrations
If you already have QuickBooks products, then QuickBooks Payroll is a natural choice as it naturally integrates with other QuickBooks products. In addition, QuickBooks Accounting integrates with hundreds of programs, including specialty programs for industries—like trucking management software. It can then pass that information to Payroll.
Best for Ease of Use & Customer Support: Square Payroll
When it comes to ease of use, Square Payroll beats QuickBooks Payroll—but only by a small margin. Although both have live support, extensive help sections, and intuitive customizable interfaces, Square is the easier interface and offers setup help, something QuickBooks only does in its Elite Plan. Further, Square’s how-to articles are easy to understand and search. QuickBooks lumps together its help articles for all its products and versions making it difficult to navigate.
Square Payroll vs QuickBooks Payroll: What Customers Think
- Square Payroll: As of this writing, Square averages 4.66 out of 5 stars with about 590 user reviews on Capterra, G2, and TrustRadius. Users praised the ease of setup and use, especially when it comes to tax forms. One issue was if they had to shut down during the pandemic and start again. Square did not issue tax forms when accounts were closed and had a hard time connecting the different accounts.
- QuickBooks Payroll: As of this writing, QuickBooks Payroll averages 4.46 out of 5 with about 700 ratings on Capterra and G2 (none on TrustRadius). This is very close to Square’s rating. QuickBooks users praised the ease of use, especially for vacation tracking, although several said customer support is “hit and miss.”
Need help selecting a payroll service? Our guide on how to find the right payroll solution contains essential tips for choosing the best one for your business.
Best Mobile Solution: QuickBooks Payroll
QuickBooks placed No. 1 in our review of the best payroll apps for mobile. You can pay and electronically file payroll taxes through QuickBooks Payroll’s mobile app, whereas Square’s app doesn’t allow it. Most of the other mobile features are the same. Both Square and QuickBooks Payroll have apps that are highly rated for Android and iOS. Both let you set and approve payroll, view time cards, track time off, and do other basic functions. QuickBooks also lets you see up to a year’s worth of past checks and view employee details.
- QuickBooks Payroll: 4.3 out of 5 on iOS (1,500+ reviews) and 4.1 out of 5 on Android (1,900+ reviews) Main praise: Fast & convenient. Biggest complaint: Login issues.
- Square Payroll: 4.8 out of 5 on iOS (4,600+ reviews) and 4.5 out of 5 on Android (780 reviews) Main praise: Ease of use. Biggest complaint: Varied, some were about Square POS and not Payroll.
How We Evaluated Square Payroll vs QuickBooks Payroll
To evaluate Square vs QuickBooks for payroll, we looked at the most common areas of concern for small businesses, from pricing and features to ease of use. We looked not only at the most important payroll functions but additional tools like HR and access to experts in case you have questions about payroll in your state.
Based on our criteria, QuickBooks Payroll beats out Square, although they are closely matched.
Click through to see the full evaluation criteria.
25%
Pricing
25%
Payroll & Reporting Features
25%
Ease of Use
10%
HR Features & Employee Benefits
10%
Popularity
5%
Reporting
25% of Overall Score
We gave higher points to the service with the lower price, but we also considered transparency, multiple plan options, and whether there are extra fees involved. While both earned perfect scores for pricing, Square has the cheaper plans.
25% of Overall Score
We considered features like automatic payroll runs, payroll tax filing, W2 and 1099 form preparation, manual check capabilities, and two-day direct deposits. We also gave points if a provider offers both employee and contractor payroll services, including a penalty-free guarantee. QuickBooks Payroll beat Square Payroll by a hair, primarily because of its quick payroll payments for customers, regardless of where they house their cash accounts, i.e., bank accounts, Cash App, etc.
25% of Overall Score
Obviously, we rated on whether the software has a user-friendly, intuitive, and customizable platform, but we also considered how it integrates with common third-party systems. We also gave points for how-to guides, live phone support, and quick resolution of client issues. The two scored well, with Square just slightly higher because it has better how-to guides.
10% of Overall Score
Having access to a professional who can provide expert advice on compliance issues is one of the top criteria here, and we considered new hire state reporting, online onboarding, and a self-service portal. Next, we looked for employee benefits, such as health insurance and workers’ compensation. QuickBooks Payroll won in this area because of its access to robust HR support.
10% of Overall Score
First, we looked at reviews that users left on popular third-party sites like G2, Capterra, and TrustRadius. Then, we tallied the ratings. Square and QuickBooks scored the same on our rubric, although Square’s user ratings were slightly higher.
5% of Overall Score
We compared the number of canned reports and the ability to create new reports within the payroll software. QuickBooks has the most premade reports and earned the higher score.
*Percentages of overall score
Bottom Line
Both Square Payroll and QuickBooks Payroll provide excellent payroll systems, with strong features for payroll that are easy to implement and use. They have mobile apps that make it easy to do payroll on the go. Both work best with their native systems: Square Payroll with Square POS, and QuickBooks Payroll with QuickBooks Accounting.
In the battle of Square vs QuickBooks for payroll, QuickBooks Payroll is the best overall payroll program. It offers plans to grow with you, next-day and faster direct deposit, a wide variety of reports, and more. Visit QuickBooks Payroll and get started today.
