While calculating employee’s hours and cutting paychecks, are you certain you’re calculating the payroll taxes appropriately? Are you in compliance with the state and federal employment guidelines?

Working out this incorrectly can lead to penalties or lawsuits. You’re on a budget and might not afford to pay a full-time bookkeeper. Luckily, many payroll software can help you do the work for you at little bookkeeping costs. A productive team is the key to a profitable business and ensuring them they’re being paid on time is the fundamental element of their performance. This is why having the best payroll software for your small business is essential.

Whether you’re looking for free payroll software, or paid full-service payroll software, there are many distinctive options available for you. Check out our top picks for the best small business payroll software to choose one that works for you.

Best Overall: Gusto

Gusto is a beautifully designed, full-service cloud-based payroll software that makes it easy to hire, pay, insure, and support your team with numerous features and a positive reputation.

Gusto has three different plans: Concierge ($12/mo per person plus $149/mo base price), Complete ($12/mo per person plus $39/mo base price), and Core ($6/mo per person plus $39/mo base price). Every plan includes the following features:

  • Automated payroll, taxes, and filings (Automated taxes, Payroll on AutoPilot, W-2s and 1099s, New hire reporting, Child-support garnishments, and Tip credits: minimum wage adjustment)
  • Filing of all federal, state, and local payroll tax forms (Form W-2, Form 940, Form 1099, Form 941, Form 8974)
  • Flexible payroll features (Multiple states, Unlimited payrolls, Contractor payments, Unlimited bonus, and off-cycle payrolls, Easy cancellations, Flexible payment schedules, Net-to-gross calculations, Multiple pay schedules Deductions, Hourly and salaried employees¸ Multiple pay rates, Garnishments, Reimbursements)
  • Advanced payroll features (Payroll reports. Accounting integrations, Integrated pre-tax benefits¸ Federal R&D Tax Credit, Time-tracking integrations, Expense integration, FICA Tip Credit for restaurants)
  • Employee management (Direct deposit, Paperless employee onboarding, Digital paystubs, Charitable donations, Lifetime accounts, Teams, Vacation and sick policies)
  • Online and on the go (No payroll setup fees, Mobile, Digital signatures, Calendar sync, Collaboration)

Most software providers charge extra fees for automatic tax filing, wage garnishment, and workers’ compensation features, making Gusto overall the best payroll software for small business owners.

Gusto also offers extra benefits like 401(k)s, FSAs, HR and administration services, setting up tax-advantaged spending team accounts, that other providers don’t offer.


  • Automatic local, state, and federal payroll tax filing
  • Unlimited payroll runs in every state
  • Remarkably great online review and ratings


  • Limited PTO and holiday pay features in Core plan
  • Support is only available to daytime hours on weekdays (8 a.m. and 5 p.m. Pacific standard time)
  • Email requests response time is around 48 hours


Best Interface: QuickBooks Payroll

QuickBooks, is well-known high-quality accounting software, making it a solid choice for small business payroll. Whether you just starting or moving your existing books, there are many QuickBooks® Online subscription options to fit your business needs. The overview and features of QuickBooks five different subscription plans are as follows:

QuickBooks Online Self-Employed

  • This plan is specifically for independent contractors and freelancers who file a Schedule C form with their 1040 at year-end.
  • The cost of QuickBooks Self-Employed is $15 per month.
  • This allows you to separately import and categorize your business and personal transactions from your bank accounts and credit cards.
  • It also helps estimate quarterly tax payments to avoid late fees.
  • Automatic track mileage via a mobile app.
  • Use QuickBooks’ receipt capture tool to record your expenses and maximize tax deductions.
  • Use QuickBooks Payments option to create and send invoices to track sales, and accept credit cards and bank transfers from customers within the invoice at additional fees.
  • Invite your accountant to evaluate your books at no extra cost
  • Connect to TurboTax to file your state and federal returns at additional fees.
  • 24/7 Customer Support via live chat and email.

QuickBooks Online Simple Start

  • The plan is best suited for sole proprietors, LLCs, partnerships, and other types of small businesses with a configuration of 250 chart of accounts.
  • The cost of QuickBooks Simple Start is $25 per month.
  • Track income, expenses, accounts receivable, sales, and monitor cash flow.
  • Import and categorize transactions from your bank accounts and credit card accounts
  • Lower data entry and keep books current by connecting with thousands of financial institutions.
  • Unlimited estimates, invoices, and sales receipts. You can also use sales form templates to create custom invoices, with three custom fields.
  • Automatic calculations and filing of sales tax
  • Use QuickBooks’ receipt capture tool to upload, email, or take photos of your receipts
  • Use mobile app to create and track sales transactions
  • The subscription is for one user, but you can invite two accounting firms to assess your books at no extra cost.
  • Run 20+ reports to monitor your business health. You can also email your scheduled reports automatically, even to non-QuickBooks users.

QuickBooks Online Essentials

  • You can manage multiple users, add three users, and configure their access. You can also invite employees and contractors to enter their hours with time tracking-only access.
  • Easily run reports to see billable time by customer and review time entries.
  • Add, review and pay vendor bills and track accounts payable with detailed reports.
  • Automatic vendor bill payments with Bill Pay at extra
  • Create recurring transactions, invoices, sales receipts, bills, on a schedule, as a template, and with reminders.
  • Track income and expenses in multiple currencies for international transactions.
  • Run 40+ reports to monitor your business health.
  • Review detailed financial reports and share custom reports with other users.

QuickBooks Online Plus 

  • Multiple user management with addition up to five users.
  • Review specific business segments with classes and location tracking
  • Track inventory using first-in, first-out (FIFO) valuation and easily review quantity on hand.
  • Create PO, receive products via payment or bill, and monitor stock status.
  • Run reports for stock counts and create inventory adjustments, as needed.
  • Mark expenses as billable to pass through to customers and projects.
  • Budgets creation and monitor income and expenses.
  • Run budget vs. actual reports to measure performance.
  • Run 65+ reports to monitor your business health.
  • Detailed reporting, transactions tracking, inventory management, budgeting, and more.

QuickBooks Online Advanced

  • Combines the features of Simple Start, Essentials, and Plus, with more additional features
  • Multiple user management with addition up to 25 users and up to three accounting firms.
  • Create multiple invoices at once for batch processing with Accelerated invoicing.
  • Unlimited classes and location tracking, track transactions across business segments.
  • A subscription to Fathom—a $468 per year value.
  • Priority Circle support including a dedicated support manager
  • Five online QuickBooks courses at $2,000 value to learn QuickBooks Online.


Most Affordable: Wave

Wave is another best accounting software for small businesses with an eccentric range of free accounting services. It’s the most cheapest payroll services out there.

Wave has two free service plans: Accounting Software at no setup fees, hidden charges or monthly fee with features like unlimited bank and credit card connections, income and expense tracking, guest collaborators and run multiple businesses in one account. Another plan is Receipt Scanning at no setup fees, hidden charges or monthly fee with features like unlimited receipt scanning with free mobile apps, capture receipts when you’re offline and automatic recording of as accounting transactions.

There are other two plans of Wave: A Self-Service Plan and a Full-Service Plan. Both these plans have locality requirement. In most states, Wave offers its self-service payroll plan at the base price of $20 plus $4 per employee and $4 per contractor per month. The features include fast and easy employee payments, workers compensation coverage, W-2 and 1099 tax form preparation, and great customer service.

Wave’s full-service plan is available in eight states only (California, Florida, Illinois, New York, North Carolina, Texas, Virginia, and Washington) at the base price of $15 plus $4 per employee and $4 per contractor with features like filing local, state, and federal income taxes with a 100 % accuracy.


  • Cheapest $20 per month price
  • Quick and easy integration with Wave’s free accounting software
  • Employee W-2 and paystub access


  • Automatic tax filing is limited to eight states only
  • Limited customization features



Basic for Payroll, HR & Tax: ADP

With 700,000+ clients around the globe, ADP is another best payroll software for small businesses. ADP is a professional employer organization (PEO) which is an HR company that helps businesses manage their HR, so they can focus on operations.

ADP offers four full-service payroll plans to manage services like direct deposit, automatic payroll tax filing, and W-2 submissions. The plans include Essential Payroll (For startups and established companies), Enhanced Payroll (For basic payroll plus wage garnishment payments, SUI and labor law posters), Complete Payroll & HR Plus (For Payroll plus employee handbooks, background checks, and our HR Help Desk) and HR Pro (Payroll plus enriched HR support and benefits for business and employees).

The pricing for all these plans is not listed on their website—you have to fill a form directly to get a quote. ADP is a suitable option for small and midsize businesses instead of large enterprises.


  • Unlimited payroll runs
  • Basic HR features in every package
  • No-penalty guarantee


  • No online pricing
  • No wage garnishment with essential payroll plan


Best Reporting: Paychex Flex

Paychex Flex is a cloud-based payroll and HR software for small businesses to help them with Payroll and outsource HR. The best features of this payroll software includes robust reporting, automatic payroll tax filing, hefty HR help, dedicated experts, and employee financial wellness program that also included in the cheapest plan as well.

And the best part: It offers massive 160+ reports with its payroll and HR packages. Of course, these reports are included in the two priciest plans. Moreover, custom analytics and reports are only available in the most expensive plan.

Just like ADP, it doesn’t have pricing available online, so it’s a good guess that Paychex is more costly than other payroll software. Which is why it is most suitable for midsize and large businesses.


  • Detailed payroll and HR features
  • 160+ & custom reports
  • New-hire reporting with every plan


  • No online pricing
  • No paper check payments with the cheapest plan



More Payroll Software Solutions for Small Businesses

We have already listed our top five picks above, but here are few more options to help you decide what suits you best based on your needs. The payroll software industry is a crowded one, and after reviewing many other providers, we have found five more small-business payroll solutions worth looking into.

  • Square Payroll

Square Payroll is a package product for almost every type of business with a contractor payrolls plan starts at $34 per month. Square offers fair pricing, automated tax filing, employee benefits, insurances, employer resources, and many time-saving tools.

With their bare-bonus plan, you can easily pay contractors or freelancers for only $5 per contractor per month, without any monthly fee. The Square payroll service is simple and affordable, and you can purchase it as a stand-alone service that works with Square’s POS solutions. Your staff can clock in and log out using the Square terminals or the mobile app, and POS data in sync with your timecards and point of sale. The benefits include:

  • Easy payment to employees and contractors
  • Employee health and insurance benefits
  • Online accounts for employees
  • Online hours tracking of employees
  • Mobile app for online payment and tracking
  • 24/7 customer support
  • No additional cost to run payroll multiple times
  • Easy payroll tax and withholding tax filing


  • Patriot Payroll

Patriot payroll is another provider for small businesses that is fast, simple, and affordable. They offer a 30 days few trials and with a monthly base price of just $10 plus $4 per employee, it offers the cheapest self-service payroll provider. They have a basic payroll plan (Base Price 10.00 + $4 / month per employee) and full-service payroll plan (Base Price 30.00 + $4 / month per employee) with add one such as time and attendance and HR software at $4 per month for HR and $5 per month for time and attendance.

The benefits include:

  • Free payroll setup, employee portal and direct deposit
  • Unlimited and flexible payrolls
  • Pay over time, sick time, and more
  • Accurate payroll and tax calculations
  • Filing of W-2s, W-3s, State and Federal taxes
  • Tracking reported tips
  • Time-off accruals
  • Multiple pay rates
  • Easy to customize
  • Free workers’ comp integration


  • Wagepoint

Wagepoint is easy and user-friendly online payroll software to help pay your employees and contractors while staying compliant with the federal, state and local payroll guidelines. The base price is just $20 a month plus just $2 per employee.

When signing up, just add your payroll information, invite your employees to access their paystubs, process hourly & salaried payroll and let the payroll run with their set-it-and-forget-it feature. It’s that simple without any setup fees, year-end fees and contracts!

The benefits include:

  • Direct Deposit
  • Payroll Calculations
  • Federal, State & Local Taxes
  • 1099s, W2s & W3s
  • Wage Detail Reports
  • New Hire Reporting
  • Additional Deductions
  • Contractor Payments
  • Additional Incomes
  • Online Pay Stubs
  • 24/7 customer support


  • OnPay

OnPay offers one fee for almost everything and that is base fee of $36 /month plus $4 /month per person covering all the basic payroll services. They also provide customized payroll services to specific industries such as restaurants, farms and agriculture, nonprofits, churches and clergy, to name a few—at no extra cost. There are no hidden costs, and there’s no upgrade require ever!

The benefits include:

  • All tax filings and payments
  • W-2 and 1099 workers
  • Direct deposit
  • Unemployment insurance withholding
  • Garnishments
  • Multiple pay rates and schedules
  • Accounting and time-tracking integrations
  • Multi-state payroll
  • Pull paystubs, employment docs, and tax forms
  • Quality customer support
  • Essential HR Tools
  • PTO management
  • Organized ORG Charts
  • Integrated 401(k) retirement plans
  • Integrated workers’ comp


  • Heartland Payroll

Heartland Payroll also offers a variety of payroll features to small businesses. From clock in and log out to human resources to tax reporting, their integrated online services makes it a great payroll software for businesses that want payroll, accounting and POS support. The pricing is not listed on their website but based upon online reviews, the service is considered expensive by most small businesses.

The benefits include:

  • Payroll + HR
  • Time & Attendance
  • Integrated Solutions
  • Payroll Tax Management
  • Pre-Employment Solutions
  • ACA Reporting
  • Benefits Administration
  • Business Lending
  • Point of Sale
  • Dedicated Customer Representative


How to Choose the Best Payroll Service for Your Small Business?

Now that you’re accustomed to the best payroll software for small businesses in 2019, it’s time to choose which will be most suited to your payroll needs. While having all the above-mentioned options readily available, deciding on the best payroll software for your small business can be confusing.

Every payroll software has its own benefits and drawbacks, but eventually, it up to you to decide about what type is most suited based on your needs, costs and functionality.

Small Business Financing News │ Merchant Advisors | blog
Best Payroll Softwares for Small Businesses in 2019
Best Payroll Softwares for Small Businesses in 2019
Looking for funding to fund your small business? The road ahead is full of twists and turns because it does require a lot of time and research to locate the best funding program that suits your business. Due to theRead more
Are you looking for the best payroll solution for your small business? We have created a list of best payroll software for small businesses in 2019.
Merchant Advisors
Merchant Advisors