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.

• “AutoPilot” payroll: Gusto can automatically run payroll for recurring pay cycles. If your payroll does not change much from one pay period to the next, this can save time and cut down on routine approvals.
• Simple payroll interface and workflow: The payroll flow is easy to follow and does not bury key data fields in multiple tabs. This is helpful if you need to review employee work hours, deductions, reimbursements, and pay details without clicking around too much.
• Global contractor payments: Gusto supports contractor payments in more than 120 countries. This gives it a clear edge over providers in this guide that stay focused on domestic payroll.
• Benefits and HR tools in the same system: Gusto goes beyond payroll by combining benefits administration and basic HR support in one platform. For a small business, that can mean fewer logins, fewer disconnected workflows, and less manual updating between systems.

Gusto limitations

Gusto is not the strongest choice if you require advanced reporting and more detailed workforce analytics. Its reports are useful for day-to-day payroll tasks, but they are not as flexible or insight-heavy as what you get from a platform like Paycor.

It can also feel less efficient as your headcount grows, especially if you need more complex workflows for onboarding, time tracking, or reporting. At that point, a more robust HR platform may be a better long-term fit.

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 Workforce, 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 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 tiers grants you access to QuickBooks Time, which comes with time and basic scheduling features.

QuickBooks Time also includes geolocation, geofencing, and mobile time clock tools. This is helpful if you employ mostly field workers. 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 offer equivalent time tracking and scheduling support—although Paycor’s are add-on modules while Gusto’s scheduling tools are limited.

• Contractor and vendor billing: Bundling QuickBooks Workforce with QuickBooks Online lets you run contractor payroll and vendor bill payments from the same system. You can create a list of vendors, set up multi-conditional approval workflows, and log bills by categories to assist with expense management. 
• Automated general ledger mapping: Payroll entries are not just synced automatically. You can control how wages, taxes, and expenses are categorized. This gives you more flexibility than most payroll tools, which offer limited mapping options.
• Project-based cost tracking: Available in QuickBooks Workforce’s higher tiers, this allows you track payroll costs by project or job, which helps with budgeting and profitability analysis. For service-based businesses, this feature is more useful than standard payroll reporting.
• Fast direct deposits: QuickBooks Workforce is the only provider in this guide that offers next-day direct deposits in its starter plan. With Gusto, you either have to pay extra for it if you’re on its basic tier or upgrade to a higher plan to get next-day payouts for free.
• “Payroll Agent” assistant: This AI tool flags payroll issues before you finalize a pay run. It also sends a ready-to-review payroll draft by text with key insights, which cuts down on manual review.

QuickBooks Workforce limitations

QuickBooks Workforce is not built as a full HR platform. It does not include tools for recruiting, performance management, or structured onboarding, which you would get with Gusto or Paycor.

Some features are split across separate apps, such as QuickBooks Time, which can make the experience feel less unified compared to all-in-one platforms. It is also capped at 150 employees, so growing businesses may need to move to a more scalable system over time.

OnPay is built for small businesses that want payroll and basic HR tools in one place without a long setup process. It supports multiple pay schedules and pay methods, enabling it to handle the payroll basics for a range of small business setups. 

It also includes HR tools that help with day-to-day admin work, such as leave management, organizational charts, employee records, and customizable onboarding tasks. These are practical features for small teams that want to keep payroll and core employee paperwork in one place without adding another system.

While it may not have automatic payroll features, its interface is straightforward, requiring just as many (or fewer) clicks as Gusto to complete pay runs. However, it doesn’t offer a contractor-only plan like QuickBooks Workforce and Gusto.

• Industry-specific payroll setup: OnPay can handle the payroll needs of various businesses and organizations, like nonprofits, churches, and agriculture companies. That gives it a more tailored feel than general-purpose payroll software.
• Compliance task monitoring: OnPay has custom personnel checklists to help you monitor employee compliance requirements. If a document expires or a task is left unfinished, OnPay sends an alert so you can follow up and catch issues early.
• Report builder: In addition to pre-built reports, OnPay lets you create and save custom report views. You can filter data fields and rearrange columns without exporting the report first. That is more flexible than systems that make you rerun reports every time you want a different view.
• Automatic org chart updates: Included in OnPay’s HR add-on, this feature automatically changes the system’s visual org chart based on edits or updates made to employee profiles. 

OnPay limitations

OnPay does not include native time tracking or scheduling, so businesses with hourly teams may need an integration like When I Work and Deputy. QuickBooks Workforce can be a better fit if you want time tracking tied more closely to payroll.

It does not support global payroll or international hiring. If that is on your roadmap, Gusto gives you more flexibility. It also lacks the deeper analytics, broader integrations, and advanced workforce tools that Paycor offers.

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 a stronger long-term fit for companies that expect their HR needs to expand beyond pay processing.

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 a worker’s gross pay so the net pay is a specified amount, like in the case of employee bonuses. Plus, Paycor has alerts for shortfalls, no pay, earnings, and hours based on your company’s needs.

• Earned wage access and paycards: Paycor gives employees more ways to access pay through OnDemand Pay, the Paycor Visa Card, and mobile wallet tools. This gives employees more flexibility than payroll systems that stick to standard direct deposit and paper checks.
• AI-powered analytics and benchmarking: Paycor goes beyond standard payroll reporting with benchmarking, predictive insights, and an AI analytics assistant. These are critical, especially if you want payroll data to support broader workforce decisions.
• Payroll tax and compliance support: If you’re dealing with more complex compliance rules, Paycor’s payroll tax compliance tools and proactive alerts can help you stay on top of payroll obligations and changing regulations.

Paycor limitations

Paycor offers more flexibility, but it is not the easiest payroll system in this guide to learn. The pay grid gives experienced users more control, though it can feel less intuitive for small teams that want a simpler step-by-step process. Gusto and OnPay are easier starting points for businesses without dedicated payroll support.

It is also a U.S.-only platform, so it is not a fit for businesses with international payroll or hiring needs. Gusto gives you more options if global contractor payments or EOR support are on your roadmap.

Cost is another tradeoff. Several of Paycor’s HR and workforce tools are sold as add-ons, and the lack of transparent pricing makes it harder to estimate total cost before talking to sales

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, payments, and filings—provided you sign up for the full-service plan. It supports 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. 

Patriot also offers add-ons for time tracking and HR tools to manage employee data. However, the HR functions are limited compared to the other small business payroll in this guide.