QuickBooks Payroll Review: Pros, Cons, Alternatives

QuickBooks Payroll is a solid choice if you already use QuickBooks Online and are looking for payroll software that will make your life just a little easier. Designed for businesses between one and 50 employees, it integrates directly with QuickBooks Online, can run payroll automatically and offers same-day or next-day direct deposits. It comes with three plans, and businesses can upgrade as they grow and require more services. Health benefits and retirement plans can be incorporated with any subscription.

However, if you use accounting software other than QuickBooks Online or have employees in multiple states, it’s worth taking a closer look at the competition. QuickBooks Online is the only accounting software QuickBooks Payroll integrates with, and if you have employees in more than one state, you may have to pay extra monthly tax filing fees.

QuickBooks Payroll is a cloud-based payroll software that allows businesses to pay employees, file payroll taxes and manage employee benefits and HR in one place. The software saves time by automatically calculating, filing and paying federal and state payroll taxes.

After getting set up, you can automatically run payroll for your salaried employees. Or, if you don’t like the automated option, you can run payroll manually from your computer or through the mobile app. You can also customize reports to include deductions and contributions, multiple work sites and paid time off.

Next-day or same-day direct deposit

Free next-day direct deposit makes QuickBooks Payroll’s lowest-tier Core plan stand out among competitor plans that include two-day direct deposits or slower. Upgrading to a Premium or Elite plan gets free same-day direct deposit for employees, a feature some competitors don’t offer at all. A quick direct deposit turnaround time is ideal for cash-flow management and means your small business can hold onto that cash for longer.

Automatic payroll

Every QuickBooks Payroll plan has the option to automatically run payroll for salaried employees paid via direct deposit. Before payroll runs each pay period, you’ll get a preview email with the opportunity to make changes. Once your employees are paid, QuickBooks Payroll will send you a confirmation text.

QuickBooks integrations

Accounting

QuickBooks Payroll integrates with QuickBooks Online so that accounting records are automatically updated alongside payroll. This allows you to see exactly how much you’re paying employees versus how much money the business is making in real time. The integration also means you don’t have to export payroll info manually and risk making mistakes in the process. You can tack any QuickBooks Online plan (from Simple Start to Advanced) onto any QuickBooks Payroll plan and vice versa.

Time tracking

QuickBooks Payroll Premium and Elite plans come with QuickBooks Time, which lets employees clock in and out on their smartphones. The Elite plan also includes a geofencing feature that notifies employees to clock in and out based on when they arrive and leave a job site. The feature can help with job costing for project-based businesses like landscaping companies, where employees work in different locations depending on the project.

Accuracy guarantee

All QuickBooks Payroll plans come with an accuracy guarantee. If a user provides accurate information on time and something still goes wrong, QuickBooks will deal with the payroll tax penalties.

The Elite plan goes a step further and covers up to $25,000 per year in payroll tax penalties resulting from mistakes an employer might have made. In other words, you’re covered even if QuickBooks isn’t responsible for the error.

Some features available only on higher-tier plans

If you have employees in different states, you’ll incur additional charges unless you have the highest-tier Elite plan. QuickBooks Payroll has a $12 monthly fee for every filing obligation outside of the primary state. For businesses with remote employees, these multiple-state-filing fees could really add up.

QuickBooks Payroll also requires a higher subscription tier for payroll setup services, unlike some other options. Its Elite plan will assign an expert to get it done, as long as you give them the required documents beforehand. And if you want reassurance that everything has been set up correctly, the middle-tier Premium plan comes with an expert review to catch any mistakes you might have made in the setup process.

Limited integrations without QuickBooks Online

QuickBooks Payroll integrates with SimplyInsured for health insurance, Guideline for retirement plans, Mammoth for HR and other Intuit products. But beyond that, choices are limited for exploring other outside add-ons. That’s part of the reason why pairing QuickBooks Payroll with QuickBooks Online makes such a difference. The accounting software integrates with over 650 other business apps that open up more time-tracking, analytics, employee benefit and customer relationship management (or CRM) options.

» MORE: NerdWallet's best small-business apps

Gusto

Pricing: Starts at $39 per month plus $6 per person per month.

Pros: For payroll software that puts emphasis on HR and employees, Gusto covers the bases. Gusto’s Concierge plan includes an employee handbook builder, along with templates for job descriptions, HR guides and policies. Those features aren't part of the middle-tier Complete plan, but it does offer access to employee surveys, coworker directories and time tracking. Unlike QuickBooks Payroll, Gusto allows for several third-party integrations and doesn’t charge extra fees for out-of-state employees.

Cons: While Gusto offers a wide variety of features, the highest-tier Concierge plan is pricey at $149 per month plus $12 per month per person. Even so, Gusto’s least expensive Core plan still includes hiring and onboarding tools.

Paychex

Pricing: Paychex Go is $59 per month plus $4 per employee per month. The higher-tier plans, Paychex Flex Select and Paychex Flex Enterprise, are custom-priced.

Pros: Paychex’s higher-tier plans come with some neat features not commonly seen from competitors, including QuickBooks Payroll. These include e-learning courses, employment verification services, an employee financial wellness program and digital marketing services.

Cons: If you need to pay employees within the next day or two, the Paychex Flex plans might not cut it. Though it’s nice to have an expert set up your account and walk you through it, the process can take 48 hours or longer. While the lowest-tier Paychex Go plan can be set up and run in under 24 hours, it doesn’t come with HR and accounting integrations.

RUN Powered by ADP

Pricing: Custom pricing based on the business’s size and desired features; rates start at $59 per month plus $4 per employee.

Pros: Compared to QuickBooks Payroll, RUN Powered by ADP integrates with a wider variety of HR solutions, accounting software and enterprise resource-planning options. The lowest-tier Essential plan also includes new hire onboarding, as well as the option to add time and attendance tracking, retirement plans, workers’ compensation, health insurance and marketing assistance.

Cons: It’s difficult to compare ADP payroll software plans against other companies because it doesn’t provide prices upfront. You also have to opt for the second-highest of four plans if you want basic HR support.

Patriot

Pricing: $30 per month plus $4 per employee per month.

Pros: Patriot’s full-service payroll plan is significantly less expensive than QuickBooks Payroll. It also offers similar features like guaranteed tax filing accuracy, HR options, time-tracking integration, 1099 e-filing and unlimited payrolls. This plan also includes free setup, a feature that only comes with QuickBooks Payroll’s $125-per-month Elite plan.