5 Best QuickBooks Payroll Alternatives for 2025

Gusto: Best overall

As a payroll software, Gusto has many of the same perks as QuickBooks, such as automatic salary and tax computations, wage garnishments, and automated tax filings. However, it has a broader range of HR features to streamline the employee lifecycle. It can post jobs, onboard workers, track attendance, plan work shifts, and monitor performance reviews.

Gusto can also pay international contractors in over 120 countries. And with its employer of record (EOR) service, Gusto Global, it can compliantly hire and pay workers in Australia, Brazil, Canada, Germany, India, Ireland, Mexico, the Netherlands, the Philippines, Portugal, the United Kingdom, and Spain (as of this writing).

Pricing

QuickBooks Payroll and Gusto offer three plans, but Gusto’s starter tier is slightly cheaper. It only costs $40 plus $6 per employee monthly, whereas QuickBooks Payroll’s starter plan is priced at $50 plus $6 per employee monthly. Plus, Gusto’s starter tier has more HR features, such as basic paid time off (PTO) policies, custom offer letter templates, and onboarding checklists.

Here are its pricing plans:

• Simple: $40 base fee per month plus $6 per employee per month.
• Plus: $80 base fee per month plus $12 per employee per month.
• Premium: $180 base fee per month plus $22 per employee per month.

It also offers a contractor plan if you only pay contract workers.

• Contractor only: $35 base fee per month plus $6 per worker monthly.

While Gusto’s contractor plan isn’t as affordable as QuickBooks Payroll’s ($15 monthly for up to 20 workers plus $2 per additional worker), Gusto includes new hire reporting in its package. This can save you time, especially if your business is located in California or a state that requires companies to report newly hired contract workers.

Gusto pros and cons

When to choose Gusto over QuickBooks Payroll

Gusto is my top QuickBooks Payroll alternative mainly because of its feature-rich platform. It’s great if you want a payroll system that can manage hiring to onboarding tasks with ease. QuickBooks doesn’t have an applicant tracking system (ATS) to monitor candidates, and its onboarding features aren’t as extensive. With Gusto, you can track applicants, create virtual welcome cards for new hires, manage email and software access, and run background checks via Checkr directly from its platform.

When it comes to payroll taxes and tax filings, both will calculate federal, state, and local taxes, but only Gusto includes tax payment and filing assistance across all levels in its starter tier. With QuickBooks, you must upgrade to at least its Premium plan to get automated local tax filing services.

Gusto’s functionalities also extend beyond just processing US and global payroll. It can help with state tax registration and offers an R&D tax credit service that lets you save up to $250,000 in payroll taxes each year. So, between features and pricing, I consider Gusto the top alternative to QuickBooks Payroll for most small businesses.

OnPay: Best value for money

What sets OnPay apart from QuickBooks Payroll and the others on my list is its flat-rate pricing. You only get one plan, with all its features and services included in that package. So, you never have to worry about whether or not a specific functionality will cost you extra or require a plan upgrade.

OnPay’s simple pricing also gives you plenty of bang for your buck. For a monthly fee of $40 plus $6 per employee, you get full-service payroll, access to benefits plans, employee self-service tools, and essential HR and team management features. As an added perk, OnPay provides white-glove setup and data migration support to get you started ― at no extra cost to you. So, even if OnPay isn’t the cheapest or lacks global payroll services, it still offers a good balance between pricing and features.

Pricing

OnPay has just one plan, with all features included. It costs $40 per month plus $6 per employee, which is slightly less expensive than QuickBooks Payroll’s starter tier ($50 plus $6 per employee per month). Similar to Gusto, OnPay offers more HR functionalities than QuickBooks.

However, OnPay doesn’t have a separate contractor-only plan. You have to pay the same rate as its full-service payroll tier, even if you only need to process contractor payments. I recommend using Square Payroll if you want a QuickBooks Payroll alternative that offers a low-cost contractor package.

OnPay pros and cons

When to choose OnPay over QuickBooks Payroll

OnPay made my list of the top alternatives to QuickBooks Payroll because of the range of core HR features that it provides. In addition to its HR information system (HRIS) module to manage employee data and documents, you get a searchable company directory and online org chart that automatically updates based on changes to OnPay’s employee profiles.

I also appreciate its customizable time off policies, which allow you to create up to three accrual rules. This enables workers to earn PTO credits at different rates depending on various factors like employee type, tenure, and work location. While QuickBooks also has customizable accrual policies, it isn’t as flexible as OnPay’s.

Further, creating payroll reports is easier with OnPay. You can add or remove a column, drag and drop it to your desired position, and use filters to select items. You can even add one of its collapsible “smart column” groups, which contain multiple columns of related data, such as work hours and employer taxes. This provides quick access to payroll info you may need to review online reports without these columns taking too much space on the report. With QuickBooks, you don’t get similar customization options.

Square Payroll: Best for contractor payments

Square Payroll is a good option if you’re looking for a QuickBooks Payroll alternative with an affordable contractor-only plan. It may not be as cost-efficient as its competitor, but it’s the cheapest on my list for a monthly fee of only $6 per worker. It includes everything you need to run payroll while staying legal and compliant, like no-fee tax form processing for your 1099s. And given the price, Square Payroll gives you plenty of value ― especially if you want an intuitive pay processing platform for you and your contractors.

However, it lacks the comprehensive HR features and international payment tools that similar payroll providers offer. It’s also best used with other Square products, like Square POS. This allows you to maximize its payment functionalities while leveraging the direct integration between its payroll and point of sale (POS) systems for easy data transfers and employee tip or commission processing.

Pricing

With Square Payroll, you get two options:

• Full-service payroll: $35 base fee per month plus $6 per employee per month.
• Contractor-only payroll: $6 per worker per month.

Compared to all of the providers on my list, Square Payroll offers the most affordable full-service payroll and contractor-only payroll plans. You can save more with this QuickBooks Payroll alternative, provided you only need basic HR tools, such as simple new hire onboarding, scheduling, and time tracking features.

Square Payroll pros and cons

When to choose Square Payroll over QuickBooks Payroll

If you have a restaurant or retail shop, using Square’s products can simplify your payment processes and operations. For example, you can use Square Online to manage your online store and once you have a physical store, get Square POS to accept payments and Square Payroll to process staff payouts. Its marketing products also help you build client relationships through email and text marketing campaigns. While QuickBooks may have several products, these are focused on payment and accounting solutions.

Unlike QuickBooks Payroll, which doesn’t have a downloadable app, Square Payroll has separate apps for employees and employers. The app for employees functions as a self-service tool where your staff can access payslips and tax forms, check schedules, get real-time messages, and clock in/out for work. Meanwhile, the app for employers allows you to import timecards, send payments, and manage payroll.

In terms of contractor payouts, you can also use the Square Payroll app to process payments for contract workers. You can even pay them by manual check, direct deposit, or via the Square Cash App. With the QuickBooks contractor payments plan, your payment option is only through direct deposits, which can be limiting, especially if you have workers who prefer to receive their pay via paychecks.

Paychex Flex: Best for dedicated payroll support

Paychex offers a wide range of HR and pay processing products for businesses of all sizes. Its core payroll software is Paychex Flex, and depending on the plan selected, you also get basic to advanced HR tools. Paychex even offers a learning management system (LMS) that you can add to its payroll platform for a fee. This is great for keeping employees engaged while increasing their skills.

It also provides access to dedicated payroll specialists who can answer your payroll-related questions and assist with payroll runs. This sets Paychex Flex apart from QuickBooks Payroll and the others on my list. With a dedicated specialist who knows your unique payroll and business needs, you can save time explaining your situation and get answers quickly. Your dedicated specialist can also uncover pay and tax issues you may have missed.

Pricing

What I don’t like about Paychex is its non-transparent pricing. You have to call its sales team to request a quote. And if you’re getting other tools, like its time-tracking module, you need to contact a separate team to get pricing details. This is unlike QuickBooks Payroll, Gusto, and Square Payroll, which all list monthly fees on their websites.

Paychex also offers different custom-priced packages depending on the size of your business. It has a solopreneur tier and plans for companies with 50 to more than 1,000 employees. For small businesses with up to 49 workers, it has three packages:

• Select: Custom pricing
• Pro: Custom pricing
• Enterprise: Custom pricing

While each plan includes its own set of features, lower-tier plans offer the option to purchase extra tools, such as expense management via Expense Wire, pre-employment screenings, recruiting and onboarding, and garnishment payments — a service that Gusto offers at no extra cost. Even on the highest-tier plan, some tools, such as employee benefits, time and attendance, learning management, and HR analytics, are available only as paid add-ons.

Paychex Flex pros and cons

When to choose Paychex Flex over QuickBooks Payroll

Paychex Flex offers more payroll support tools than QuickBooks and other competitors. In addition to its dedicated payroll specialist, its Paychex Pre-check feature lets your employees review their paychecks before the scheduled pay day. This allows them to raise questions about missing pay items like overtime and, simultaneously, enables you to minimize payment errors and avoid costly payroll mistakes.

Like Square Payroll, Paychex Flex is also a good option for processing payroll while on the go. You can start pay runs via its mobile app and continue where you left off on your laptop or desktop and vice versa.

And if you’re looking for a financial wellness program, Paychex offers financial education courses and short-term loans for your employees. It even has an intuitive income calculator that lets your workers determine if their retirement plan is on track to meet their retirement goals based on the information that they provide. None of the providers on my list, including QuickBooks Payroll, have a similar retirement readiness calculator.

RUN Powered by ADP: Best for scalability

If you worry your business will outgrow QuickBooks Payroll, consider RUN Powered by ADP or ADP RUN as an alternative. It offers the full-service payroll, tax filing services, and compliance support that many of the best payroll software bundle into their plans. ADP also has a variety of HR products and services that can meet the needs of small to large businesses, making it highly scalable compared to QuickBooks and the other QuickBooks Payroll alternatives on my list (except Paychex Flex).

If you want a small business payroll system with nominal HR features, you can start with ADP RUN. Its basic plan offers a better range of HR tools than Paychex Flex and QuickBooks Payroll. If you want more features or have a bigger workforce, you can switch to other products like ADP Workforce, which is optimal for midsized to large businesses. You can also get ADP TotalSource, a professional employer organization (PEO) service that handles your day-to-day HR and payroll tasks.

Pricing

ADP RUN is another QuickBooks Payroll alternative that doesn’t list its pricing on its website. You can get a quote by contacting its sales team.

It has four plans:

• Essential: Custom pricing
• Enhanced: Custom pricing
• Complete: Custom pricing
• HR Pro: Custom pricing

While many of its HR features, such as learning management and applicant tracking, are only available in higher tiers, ADP RUN is better than Paychex Flex because it only charges extra for a handful of tools, such as time tracking, retirement and health insurance plans, and workers’ compensation. Plus, with Paychex Flex, hiring and employee onboarding features are paid add-ons, even if you get a higher plan.

RUN Powered by ADP pros and cons

When to choose RUN Powered by ADP over QuickBooks Payroll

If you need a wide range of HR features, higher-tier ADP RUN plans come with robust recruitment tools, such as ZipRecruiter job postings, applicant tracking, and background checks. You even get salary benchmark information to help you attract qualified candidates and gauge the competitiveness of your compensation package.

In addition to its LMS, which lets you assign and track the completion of online courses, it offers access to a sexual harassment prevention training program that you can readily deploy to employees. And that’s all on top of the in-app compliance alerts and HR support you get from ADP’s team of HR professionals who can help you navigate complicated HR issues. You can even access marketing tools and get legal assistance via Upnetic’s advisors and legal services.

Further, ADP RUN makes paying employees via paychecks easier. It can prepare the paychecks, stuff and seal them into envelopes, and then deliver these to your office in time for you to distribute to employees. It even offers check signing services and provides paychecks with 10 advanced fraud protection features — a functionality that QuickBooks and the others on my list don’t provide.