Best Payroll Software for Small Business

Gusto started as an employee and contractor payments company but now supports various HR functions like benefits administration, performance management, recruitment, and global payroll. As a full-service payroll company, it offers automatic deductions, remittances, and filings of federal, state, and local taxes. It can even handle minimum wage adjustments for tip credits and child support payments in 49 states (all but South Carolina). In contrast, many standalone payroll solutions for small businesses require you to process garnishments and local taxes manually. 

Gusto also supports global businesses with contractor payments in more than 120 countries. For its Gusto Global product, it partnered with Remote to offer EOR services for employers needing to hire and pay workers in the following countries:

While the coverage may be limited as of this writing, Gusto plans to expand its EOR services to other countries soon.

Gusto limitations

Even if it has started offering global hiring and payroll services, Gusto is not the most scalable solution in the market. Enterprise businesses, for example, will have difficulty finding crucial pay data insights, such as pay disparities and compensation benchmarks. This is because Gusto has limited report customization capabilities and completely lacks data visualization. Instead, you’ll need to export the reports to a spreadsheet program to create customized charts and gain data insights.

Gusto also becomes tedious to use once you have more than 50 employees. Unless you upgrade to a higher tier, it still requires some manual data inputs for things like time tracking and new hire onboarding.

Simple payroll interface

Gusto’s payroll module features a progress bar with steps and instructions at the top so you stay on track and remember what information you need for payroll finalization. If you don’t enable Gusto’s AutoPilot function, running payroll takes only three steps: enter employee earnings and actual work hours, input time off details, and review and submit. 

If you don’t have a native or integrated time-tracking module, Gusto makes the process somewhat less tedious than Rippling, which previously held the top spot in this list. This is because Gusto includes fields to adjust employees’ hours, earnings, deductions, and reimbursements on the same page. You only have to open the section to adjust the fields that apply to each employee.

This is unlike Rippling, which separates hourly and salaried employees into different steps and puts each employee’s earnings and deductions in tabs. You will need to switch tabs and do long, horizontal scrolls to find and adjust the pay codes that apply to each employee. As a result, Rippling requires significantly more clicks to finish payroll than Gusto.

Payroll add-ons

Gusto offers several add-on features that benefit small businesses. It can help you save money with R&D tax credits or start a pay-as-you-go workers’ compensation policy through its partner, NEXT Insurance. If you sign up for its state tax registration add-on, Gusto will file and monitor all the paperwork needed to expand your business into new states.

Further, Gusto has a free bill pay module. It allows you to create an electronic roster of all your vendors, upload bills from suppliers and subcontractors, and schedule payments. However, its features aren’t extensive—you can’t attribute codes, like utilities, to payments for accounting purposes or send transactions to stakeholders for approval. You also can’t filter or export bill payment data to your accounting application. Nevertheless, if you’re switching to Gusto after doing accounting and payroll processes yourself, it is a step up from manually maintaining billing and vendor profiles.

OnPay’s specialty may be payroll, but it has all the features you need to manage small business HR processes, such as time off management, benefits administration, task management, and customizable onboarding workflows. These all come standard with OnPay, unlike the other providers on my list that require you to purchase a higher subscription to get some of these features.

OnPay may not have automatic pay run features, but its interface is straightforward, requiring just as many (or fewer) clicks as Gusto to complete payroll. Like Gusto, OnPay lets you add or adjust earnings and deductions on the same screen, avoiding extra clicks and cumbersome spreadsheets. You can also adjust specific employee pay information in a sidebar window without leaving the workflow.

While it doesn’t offer a contractor-only plan like QuickBooks Payroll and Gusto, OnPay allows you to pay contractors within the same pay cycle as your regular employees. This avoids repeating the payroll process for your different worker classifications at the end of every pay period.

OnPay limitations

OnPay is not the best choice if you expect to need more robust payroll features later. It supports unlimited and multi-state payroll but lacks global payroll functionality. OnPay may flag you of payroll errors as you process employee payments, but lacks in-app compliance checkers, so you’ll have to become familiar with new laws on minimum wages, PTO, and overtime in each state where your employees reside before running payroll.

One of the biggest drawbacks, especially for businesses with mostly non-exempt hourly workers, is OnPay’s lack of native time-tracking or scheduling features. It does integrate with popular options like When I Work and Deputy, but QuickBooks Payroll may be a better choice if you want easy data transfers from time tracking to payroll.

Employee engagement and recordkeeping

OnPay offers basic staff engagement and recordkeeping features that you rarely see in standalone payroll platforms, such as employee profile bios and customizable fun fact questions. Workers can view this information and work contact numbers directly in OnPay. This is useful if you have shift workers who need to reach team members to report emergencies like tardies or other shift changes.

You can use its customizable forms to create documents for tracking business and staff information, such as collecting employee T-shirt sizes for an upcoming work event or tracking company equipment like computers and keys. Its e-signature capabilities also allow you to collect essential documents and obtain legal acknowledgments from employees. For instance, employees can electronically sign uniform deduction agreements to deduct the cost from their next paychecks.

You can even create similar flows for handbook policies, including any that impact payroll processes, such as employee bonuses, reimbursements, and other deductions. Gusto may have similar functionalities but reserves it for its higher-paying plans.

Payroll reports builder

OnPay includes a payroll-specific reports dashboard, with links to important reports, like general ledger (GL) summary and payroll register, directly on the main page. Graphs also provide quick views of the number of employees paid each month and paid wages by type to track costs and turnover.

You can save custom reports and views to access the data you need as it changes with each pay run. I was also impressed with OnPay’s report designer, which lets you filter and drag-and-drop report columns to adjust your view in real time without downloading data to a spreadsheet program of choice. This saves you time from downloading reports repeatedly. In contrast, Gusto only lets you choose the columns or data fields you want. You can’t rearrange the order without running the report and selecting the columns again. If you want an easier way of viewing and filtering data fields for your reports, use OnPay.

As a small-business accounting giant, Intuit’s QuickBooks is highly likely one of the first software products you purchase alongside a payroll solution. If you get both QuickBooks Online and QuickBooks Payroll, you can manage accounting and payroll data from the same app so you can see a single view of your business’s cash flow. Running payroll in QuickBooks is also relatively easy. It automatically populates earnings for your salaried employees, but you’ll have to manually enter regular and overtime hours for your non-exempt hourly staff. However, upgrading to its higher subscription tiers grants you access to its native time and scheduling capabilities.

In addition to attendance monitoring and staff scheduling, you get geolocation, geofencing, and mobile time clock tools. This is helpful if you employ mostly field workers without a central base of operations. Plus, as you progress subscription tiers, you access additional project tracking features.  By comparison, Paycor and Gusto are the only alternatives on my list that offers equivalent time tracking and scheduling support—although Paycor’s are add-on modules while Gusto’s scheduling tools are limited.

QuickBooks Payroll limitations

QuickBooks Payroll is ideal to use if you’re a QuickBooks user or only need a standalone payroll option for your small business. It doesn’t support third-party integration options for strategic HR functions, such as recruitment and performance management. It also lacks an organizational chart and customized onboarding workflows.

Contractor and vendor billing

If you bundle your QuickBooks Payroll subscription with QuickBooks Online, you can run payroll and vendor bill payments from the same system. QuickBooks’ is significantly more advanced than Gusto’s bill pay option. In addition to creating a list of vendors and paying them directly from the platform, it lets you set up multi-conditional approval workflows and log bills by categories to assist with expense management. This is great if you’re managing bills from multiple work locations and need certain employees to confirm bill accuracy, such as when bills exceed a certain dollar threshold.

If you don’t have employees, QuickBooks offers a contractor payments option with accounting features. Besides being more affordable than Gusto’s contractor-only plan, it doesn’t restrict you from following typical employee payroll schedules. Instead, you can pay contractors per any pay agreement you make or alongside your regular billing cadences. This provides you more control over your company costs, allowing you to schedule payments during periods of higher revenue.

General ledger integration

Exporting payroll ledgers to your accounting program of choice can be tedious, especially if your payroll platform doesn’t integrate with your accounting program. However, when you use QuickBooks Payroll and QuickBooks Online together, the system automatically records applicable pay data in your chart of accounts once you finalize payroll. While it automatically assigns default accounts to map your payroll based on wages, expenses, and liabilities, you can modify these settings to your liking.

For example, you may use a particular account to monitor your contribution to payroll taxes outside of a general expense account. Besides helping you understand your tax liabilities, you can also use it to determine some of the costs associated with hiring a new employee for recruitment and headcount planning purposes.

Paycor is an all-in-one human resources management system (HRMS) that offers modules for critical HR functions like payroll as well as auxiliary processes like learning and development. This versatility makes Paycor best suited for growing and established companies that need direct control over their payroll processes in a unified HR tech stack. 

It lets you add or modify existing payroll schedules as needed, and the system will automatically make the necessary adjustments. It has a customizable pay grid organized by rows of employees, which lets you add and remove columns for information like bonuses and commissions to fit your needs. You can even pay terminated employees without temporarily changing their employment status in the system. This is great if there was an error in the employee’s previous payroll and you need to pay them an adjustment after they’ve separated from the company.

There are also buttons to automatically adjust an employee’s gross pay so the net pay is a specified amount, like in the case of bonus checks. Plus, Paycor has alerts for shortfalls, no pay, earnings, and hours based on your company’s needs.

Paycor limitations

Paycor’s pay grid setup may increase payroll efficiency for large teams, but it can be overwhelming for small businesses and startups that need dedicated support. Without a step-by-step guide, newbies are less likely to remember to add or adjust critical pay items. Gusto, for instance, has a separate step just for keying PTO hours—a crucial data point that’s easy to miss if you’re managing payroll on top of multiple other HR functions.

Paycor also doesn’t support payroll outside of the U.S., so it’s a better option for domestic businesses with seasoned HR or payroll specialists that need flexibility over their pay processes.

Multiple employee payment methods

Paycor lets you pay employees through direct deposits, paycards, or checks. It also offers on-demand pay, allowing employees to access up to 50% of their wages before payday through its mobile app. Free budgeting, financial counseling, and learning resources for employees also compete with the financial wellness resources offered by Gusto.

Another great feature is Paycor’s check-stuffing services to pay your unbanked employees. While most payroll platforms let you print live checks, it adds extra steps to the payroll process like ensuring you have the proper check stock paper and magnetic ink to manually print checks.

Custom reports and analytics

Before finalizing payroll, Paycor populates charts so you can view key information about payroll runs quickly. Doughnut charts allow you to see the breakdown of employer and employee tax liabilities, while a series of quick links lets you download popular reports, like your payroll journal. It even pre-populates employee pay stubs up to three days before paydays, enabling your workers to check their expected payouts and report pay errors.

Paycor also has a report builder to craft customized reports from scratch. You can work off pre-existing reports by adding, renaming, or creating new columns for analysis. Many of the payroll reports also come with visualizations, like total compensation by month and department, to understand changes in labor costs without switching to your accounting software.

Further, Paycor’s analytics module includes an AI digital assistant to ask questions and receive answers about your employee data in natural language. Meanwhile, benchmarking and predictive analytics let you compare pay practices with industry standards and adequately plan for the future.

Similar to QuickBooks, Patriot offers software for payroll and accounting. Its platform has a simple but intuitive interface that helps streamline processes, making it easy for small businesses to learn and use its various features. With its payroll module, you get unlimited pay runs with automatic federal, state, and local tax deductions and filings—provided you sign up for its full-service plan. It offers several essential payroll features, such as multiple pay schedules and customizable money and deduction types, enabling you to create your own employee deductions and company-paid contributions and payments, such as special bonuses. 

If you have a multi-location business, you can assign employees to a primary work location in the system, which also includes a work-from-home option. Patriot Payroll will then calculate the applicable payroll taxes based on the employee’s work location. Plus, you don’t need to manually search for workers assigned to specific business sites when running payroll. Patriot Patriot has a filter option that lets you choose the work location, allowing you to process and review payroll only for specific teams.

Patriot Payroll limitations

Patriot Payroll may support unlimited pay runs for US-based workers, but it lacks Gusto’s global payment tools. Its contractor-only package also does not compete well with QuickBooks Payroll, which only costs $15 monthly for up to 20 workers; whereas Patriot charges $17 per month plus $4 PEPM if you’re on its basic plan. Plus, Patriot collects add-on fees for time tracking and multi-state payroll tax filings. And even if you get the HRIS add on, the features are very limited. This is unlike Gusto and OnPay, which include basic hiring tools and automated onboarding flows in their starter tiers.

While you can get two-day direct deposits with Patriot Payroll, it only offers this to qualified customers. If you don’t meet Patriot’s requirements, you will only be entitled to a four-day option. This is unlike the other providers in this guide that don’t have qualifying assessments for two-day direct deposits. However, if you require fast payouts to expedite payroll processing times and don’t need a wide range of HR tools, consider QuickBooks Payroll as it offers a next-day option in its basic plan.