Top 7 Payroll Software for Accountants

If payroll processing is an important service for your firm, then you’ll want to make payroll processing faster, easier, virtually hassle-free and highly profitable. Using Payroll software for accountants is the one of the best payroll solutions.

Best Payroll Software for Accountants

In our search for the best payroll software for accountants, we looked for solutions that easy to use. We also consider those features that would most make an accountant’s life easier. For instance, many options will guarantee flawless tax calculation and filing. This should hold true for federal, state, and local taxes.

Before making any kind of decision, it’s often best to do thorough research on the payroll solutions that may (or may not) work best for your unique needs. Does the payroll software allow direct deposit, check printing, and pay cards? Is the platform cloud-based, on-premise, or otherwise?

Here’s a roundup of our best picks to help you find the right payroll software for accountants.


Gusto - Best Payroll software for small business

Gusto is the best payroll software for accountants that combines payroll, benefits administration, HR and compliance functionalities in a single, simplified package. Designed to serve mainly small businesses across the United States, Gusto provides tools to manage core HR needs such as time tracking, hiring, onboarding and training, among others.

Payroll Key Features

  • Automated payroll filings and tax payments – The platform is capable of automating the calculation, payment, and submission of a company’s local, state and federal payroll taxes (All 50 states).
  • Direct deposit – Payments can be made via direct bank deposit or through check.
  • Ability to run payroll during the off cycle (e.g., bonuses or reimbursing employees)
  • Paying and generating year-end w-2 forms and 1099 forms.
  • Ability to calculate net-to-gross payments
  • Lifetime access to paystubs (employees can access paychecks and W-2s even after leaving the company)
  • Check printing, such as custom checks, blank checks and checks that include employee’s earning statement at top or bottom of the page
  • Integrates with other software, such as Freshbooks, Boomr, Xero or Quickbooks
  • Reporting – payroll history, bank transactions, tax payments and more

Compliance Functionalities

  • Apply for and pay workers’ compensation insurance
  • Instant workers’ compensation claim estimate with a final quote within two business days
  • Compliance checklist that’s regularly updated if new requirements set by federal, state or local agencies

Benefits Management

  • Ability to work with Gusto’s brokers to select the best benefits plan
  • Employee self-enrollment in health insurance plans via individual Gusto accounts
  • Automatic deductions for health insurance and other benefits each time payroll is run
  • Compliance with HIPAA, ERISA and Affordable Care Act
  • Notification of open-enrollment reminders

Integration With Accounting Software

The system integrates with a variety of accounting software, including Freshbooks, Xero, Aplos, and Quickbooks. You can run automatically or manually sync with other accounting software including: Total wages, taxes, benefit deductions/contributions reimbursements and contractor payments.

Access from Mobile or Table Device

Gusto is accessible from any web-enabled device. You don’t need to download an app — just sign into Gusto on your web browser.


Gusto provides an online Help Center for users to browse through articles and FAQs on payroll, taxes and other topics. They can also leave a message via the Help button. In addition, Gusto works with the IRS on the company’s behalf if there’s any payroll tax problems or other issues.


Gusto provides three pricing tiers.

  • Core – The Core plan has a base rate of $39 per month plus $6 a month per employee.
  • Complete – The Complete plan has a base rate of $39 per month plus $12 a month per employee.
  • Concierge – The Concierge plan has a base rate of $149 per month plus $12 a month per employee.

Gusto offers additional options for employee benefit and insurance.

  • 401(k) retirement plans – There is a $40 a month minimum to participate in this option, plus $8 per participant per month. There is a $500 set up fee.
  • 529 college savings plan – There’s no set up fee required, but there’s a $18 a month minimum, plus $6 a month per participant.
  • Pre-tax spending accounts – Gusto offers an annual $200 service charge that covers health spending accounts (HSA), flexible spending accounts (FSA) and commuter benefits. However, for companies that rather purchase each plan individually, HSA is $2.50 a month per participant, and FSA and commuter benefits each has a $20 a month minimum and $4 a month per participant.


San Francisco Office: 525 20th Street, San Francisco, CA 94107, USA
Denver Office: 1201 16th St, Denver, CO 80202, USA
Sales: (877) 691-3295

Visit Gusto


Run ADP Payroll Software for Small Business

RUN Powered by ADP® is fast, easy, and affordable payroll solutions for small business. It is an cloud-based payroll software and automatic tax that allow you to calculate, file, deposit and reconcile your payroll taxes. This solution also come with a tax payment guarantee that no errors will be made, and provide employees with year-end tax forms.

Key Features

  • Automatically calculates deductions for tax, health benefits and retirement contributions. In RUN, you can run your payroll or process in just a few steps.
  • Automatic electronic filings and deposits to help you comply with federal, state and local regulations. Supports all 50 states with printed/signed paper forms.  Electronic filing and payment are available for Federal and California.  Tax forms are calculated by ADP in all states with the exception of Pennsylvania and Vermont.  Local income taxes are calculated in 4,000 different jurisdictions. In RUN W-2s and 1099s created, distributed and filed for you. RUN also help responding to payroll-related requests from the IRS.
  • Time and Attendance – ADP® Time and Attendance integrated with RUN helps you simplify compliance and manage overtime to protect your bottom line.
  • Flexible Payment Options – RUN payroll software lets you choose between flexible payment options so you can pay your employees the way they want to be paid, includes: Direct deposit, Pre-paid VISA cards, ADPCheck™, and Payroll Delivery.

Compliance Functionalities

  • State Unemployment Insurance (SUI)
  • ADP’s Pay-by-Pay Premium Payment Program
  • for Workers’ Compensation
  • Wage garnishment payments
  • Labor Law poster compliance

Integration with Accounting Software

This payroll software solution offers integration with popular accounting software you may use, including: Intuit Quickbooks, Sage 50, Xero, and Wave.

  • Integration with Quickbooks – Use the ADP InfoLink General Ledger Interface website to create a payroll report that you can import into QuickBooks. You must set up QuickBooks for manual payroll before importing the ADP payroll file.
  • Integration with Xero – Once setup, you can import ADP payroll data into Xero in just a few clicks.

Mobile App

RUN ADP offers on-the-go mobile access through ADP Mobile Solutions that you can find in the Apple Store (iOS) or Google Play (Android).


Live support is available 24/7. Users can access online Contact & Support Center to browse through articles and FAQs on payroll, taxes and other topics.

RUN also comes with the support of ADP’s payroll tax compliance team with notifications for tax deadlines, changes and new requirements. The team helps to make filings and tax deposits as per the latest regulations of federal, state and local tax authorities.


ADP RUN offers three plans: Essential Payroll, Enhanced Payroll, and Complete Payroll + HR. They don’t publish their pricing plans online. However, services from similar providers have monthly fees that cost around $20-$50 for the base fee, plus an additional $2-$5 per employee. More extensive software can cost $1,000-$3,000/year.

The main differences between the plans are the inclusion of additional features such as check signing, background checks, as well as HR training and toolkits.


Sales: 800-225-5237



Patriot Payroll software for small business

Patriot is an simple and affordable online accounting and payroll software for accountants in the USA. Created by Patriot Software, this secure online payroll system helps streamline different processes associated with managing tax submissions and payroll payments.

With Patriot Payroll, organizations have the capability to issue payrolls through electronic cheques and direct bank deposits. Patriot Payroll provides robust tools to print checks, maintain payroll records, generate payroll reports, and establish direct deposits into bank accounts. It also  automatically updates tax tables, so companies don’t have the headaches of having to manually keep up with tax compliance..

Basic Features

  • Run unlimited payrolls – Companies can run an unlimited number of payrolls
  • Payroll setup & expert – support Patriot will set up your entire account for free and offers free (US-based) support via phone, email or chat.
  • Print checks or use direct deposit – Pay your employees with Patriot’s free direct deposit, or use printed or handwritten paychecks, or cash.
  • Flexible Pay Schedules – Patriot Software allows you run and pay employees as often as you need according to their pay schedule.
  • Printable W-2s – A W-2 Form is a report of all employee income and tax withheld for a calendar year. This is needed in order for the employee to file their income taxes.
  • Employee Portal – Employee portal give your employees secure access to their paystubs, pay history, and payroll information.

Full Service Features

The Full Service Payroll plan includes all of the features of the Basic plan, but it also offers tax filing service. With the Full Service Payroll option, Patriot collects, remits and files federal, state (all of the states in the USA) and local taxes on the company’s behalf. This plan also allows for filing of W2 and W3 forms, as well as guaranteed on-time tax filings.


Patriot also offers online payroll add-ons including Time & Attendance to simplify your payroll and timekeeping, and HR Software to streamline your HR process.

Integration with Patriot Accounting Software

Patriot Payroll Software can be integrated with Patriot Software’s basic, cash-basis accounting application that includes bill-paying, invoicing, and income/expense-tracking.

1099 software and contractor payments require accounting subscription. Patriot Accounting allows users to issue 1099 and 1096 tax forms as well as draft invoices for vendors and contractors.

Mobile App

Patriot Software has been developed to be “responsive,” which means that the screens are formatted to fit your phone, tablet, or desktop computer. You do not need to download an app from your mobile phone app store in order to use Patriot Software on your phone. Instead, just use your phone’s web browser and log in to Patriot.


Users can contact customer support via phone, email or chat. There is also a Help Center that contains articles and videos.


Businesses only need to pay a monthly subscription fee that they can cancel with no penalties. The fee structure is based on number of employees a business run payroll for in a given month.

  • Basic Payroll $10 per month + $4 per month per employee
  • Full Service Payroll $30 per month + $4 per month per employee
  • Time & Attendance Add-ons Start at $4 per month + $1 per employee
  • HR Software Add-ons Start at $3 per month + $1 per employee


Corporate Headquarters: 4883 Dressler Rd. NW, Suite 301, Canton, OH 44718, USA
Phone: 877-968-7147 Email: [email protected]

Visit Patriot


OnPay Payroll Software for Small Business

OnPay is a cloud-based payroll software for accountants that handles all payroll responsibilities. With this system, businesses can run an unlimited number of payrolls each month and pay both W-2 and 1099 workers by direct deposit or printed checks. The service also takes care of all payroll tax obligations, including calculating, filing and paying payroll taxes on your behalf. This solution guarantee all tax filings and payments will be made accurately and on time.

Payroll Features

  • Unlimited Pay Runs – The service allows an unlimited number of payroll runs each month for W-2 employees and 1099 contract workers. The option to run payroll at any time allows you to create multiple pay schedules for different types of employees. For example, contract workers can be paid every week and salaried employees every other week.
  • Pay Options – Whether you and your employees prefer direct deposit, pre-paid debit cards, or cutting your own checks, you can pay wages however you want without any extra fees.
  • Automated Payroll Taxes – OnPay handles all payroll tax responsibilities. The service calculates the payroll taxes each month; processes the required payments; and pays local, state, and federal tax agencies for you. In addition, the company prepares and files all quarterly and annual payroll returns. At the end of the year, OnPay generates W-2 and 1099 forms. All of the tax services are guaranteed. If a mistake is made, OnPay pays any fines or interest incurred.
  • Employee Self Onboarding – Your employees can enter all their personal details online to save you time.
  • Any Employee Type – Pay contractors, salaried employees, hourly workers, tipped workers, or agricultural workers. OnPay even handle special tax filings for clergy, and nonprofits.
  • Automatic New Hire Reportings – OnPay report new hires to the government for you.
    Lifetime Accounts – Employees can access their paystubs and W-2 forms online, even if they are no longer with your team.

Payroll deductions

OnPay also manages all payroll deductions. Deductions are calculated every pay run and listed on each employee’s pay stub. The system allows as many types of payroll deductions as you want, including:

  • Standard dollar amount or percentage deductions
  • Goal or loan deductions that stop automatically
  • 401(k), IRA and other retirement contributions
  • Section 125 or (pretax) health insurance deductions

Additional services

OnPay offers several additional services, including employee insurance benefits, workers’ compensation plans and 401(k) retirement plans.

Integration with Accounting Software

The system integrates with a most popular accounting software you may use, including QuickBooks and Xero.

  • Integration with Quickbooks – You can choose whether you would like payroll to sync automatically and if the data should come over in detail or summary form. If the information is selected to come over in detail, then you will see the transactions separated by employee.
  • Integration with Xero – Adds payroll transactions into Xero automatically.

Mobile App

OnPay Software has been developed to be “responsive,” which means that the screens are formatted to fit your phone, tablet, or desktop computer. You do not need to download an app from your mobile phone app store in order to use OnPay Software on your phone. Instead, just use your phone’s web browser and log in to OnPay.


OnPay offers customer service between 9 a.m. and 8 p.m. (ET), Monday through Friday. Users can access online Knowledge Center to browse through articles on payroll, taxes and other topics.


OnPay allows small business to conduct their payroll online through their services for $36 a month, plus $4 for each employee or contractor. Additionally, they offer printing and shipping of W-2s for $5 each plus shipping fees.


OnPay, Inc: 1230 Peachtree Street NE, Suite 1250, Atlanta, GA 30309
Phone: (877) 328-6505 9AM – 8PM ET, Monday – Friday

Visit OnPay


Wagepoint Payroll Software for small Business

Wagepoint is a new generation of payroll software for accountants designed to focus on involvement of the human connection to enable companies to issue payment to their employees more simply and efficiently. With use of advanced Wagepoint payroll software, SMB owners, financial officers, and HR management can revise their procedures for payroll processing, automating the entire operation.

Payroll Features

  • Payroll Calculations – Wagepoint automatically do the gross-to-net calculations for you.
  • Federal, State & Local Taxes – Payroll taxes are calculated and collected with each payroll. Based on your filing and reporting schedule, Wagepoint accurately submit all the taxes and reports on your behalf.
  • Direct Deposit – Once your payroll is approved four business days prior to the desired paydate by 3pm EST, your company’s bank account will automatically be debited, and your employees or contractors will receive their pay directly in their bank accounts on pay day.
  • W2/1099/W3 Reports – At year-end, Wagepoint automatically populate all W2s/1099s with the payroll amounts for the year, and the service submit them to the IRS on your behalf by January 31 each year.
  • New Hire Reporting – Federal and state laws require that all new and/or re-hired employees are reported to the government for inclusion in the State directory. Wagepoint takes care of this and submits your New Hire Reports within 20 days of adding a new employee or re-hiring an employee.
  • Additional Incomes – Wagepoint automatically calculates the tax implications of any income added to a regular pay such as bonuses, commissions, expenses, holiday pay, overtime, or really anything at all to your employee’s paycheck.
  • Additional Incomes & Deductions – Wagepoint automatically calculates the tax implications of any income added to a regular pay such as bonuses, commissions, expenses, holiday pay, overtime, or really anything at all to your employee’s paycheck. The service also easily deduct 401K contributions, health benefits, parking etc. from an employee’s paycheck. Wagepoint automatically figures out the tax implications of all the deductions.
  • Workers’ Compensation – Wagepoint have partnered up with E-Comp to offer Pay-as-you-go Workers’ Compensation plans. Unlike traditional Workers’ Compensation you don’t have to pay a deposit or down payment, and your premiums are calculated based on actual payrolls.
  • 401(k) Plans for Small Business – Wagepoint have partnered up with Ubiquity to offer two types of 401(k) retirement plans. Express(k) plans are ideal for businesses looking for an easy, ready-to-go plan, while the Custom(k) plan gives you the flexibility to maximize savings for your business and employees.

Integration with Accounting Software

The system integrates with a most popular of accounting software you may use, including QuickBooks Online, Xero, and Less Accounting.

  • Integration with Quckbooks Online – Track and manage all your payroll transactions in Wagepoint with QuickBooks Online. With this Integration, you can automatically sync your total wages, taxes, reimbursements and contractor payments.
  • Integration with Xero – You can import payroll transactions into Xero by specific pay period, time period or by invoice. You can also automatically synchronize all wages, taxes and liabilities into the right chart of accounts.
  • Integration with LessAccounting – You can automatically import your payroll invoice, complete with the net payroll amounts, tax payments as well as our fees.

Mobile App

Wagepoint Software has been developed to be “responsive,” which means that the screens are formatted to fit your phone, tablet, or desktop computer. This solution also provides Time Tracking App that available on App Store (for IOS) and PlayStore (for Android).


You can use Wagepoint’s floating ‘Support’ tab to access the app’s knowledge base or send a support ticket in case of questions. Wagepoint currently scores 95% on customer service satisfaction.


Wagepoint uses a simple pricing formula thtat includes a base fee combined with a $2 fee for each employee. For example the cost of one payroll for a company with 10 employees would be $20 + (10 X $2) = $40 per pay. To figure out your monthly costs, you then multiply this cost with frequency (for this example we’ll use bi-weekly or semi-monthly).


Waterloo: 151 Charles Street West, Suite 100, Kitchener, ON, N2G1H6
Halifax: #3-644 Portland Street, Suite #238, Dartmouth NS, B2W 6C4
New York: 85 Fifth Avenue, 3rd Floor, New York, NY, 10003
Phone: 1-877-757-2272

Visit Wagepoint

QuickBooks Full Service Payroll

QuickBooks Full Service Payroll

QuickBooks Full Service Payroll is one of the most popular payroll software for accountants in the United States available today. It is a web-based payroll system that integrates with the QuickBooks accounting platform. This solution designed to help small businesses manage accounting and payroll all in one place. All packages allow unlimited payroll runs each month and are managed on an easy-to-use online platform.

Key Features

  • Online employee setup – Users can manage employee profiles to determine such things as pay rate, pay schedule and method of payment. Your employee also can easily view their paycheck and W2s.
  • Effortless Payroll Just enter the hours for up to 50 employees and Quickbooks Full Service Payroll will process payroll for you. Choose from checks or direct deposit.
  • Payroll Taxes & Forms – Quickbooks Full Service Payroll will handle quarterly and year-end payroll taxes and forms for you.
  • Accuracy Guaranteed – Intuit promise to pay and file your taxes accurately and on time, or Intuit pay any resulting penalties.
  • Free Same Day Direct Deposit – In Quickbooks Full Service Payroll you can pay your employees faster with free same day direct deposit. Submit payroll up to 7 AM (PT) the day of payday.
  • Payroll Reports – Review your payroll at a glance with detailed reports.

Mobile App

All of Quickbooks Full Service Payroll functionality carries over to the Online Payroll mobile app, which is available on iOS and Android devices.


Intuit QuickBooks Full Service Payroll has phone and email support available from 6 a.m. to 6 p.m. Pacific time, Monday to Friday as well as 6 a.m. to 3 p.m. Pacific time on Saturday. Intuit QuickBooks Payroll also has a searchable support center with FAQs, user guides and video tutorials, although we found it cumbersome to navigate.


Intuit offers three service plans – Simple Start, Essentials and Plus – that differ in services and prices. For each plan there is a monthly base fee, plus $2 per employee. Discounts are regularly offered and a free 30-day trial is available.

  • Simple Start – $119 /mo plus $2 per employee per month. This plan includes all key features that mentioned above.
  • Essentials – $134 /mo plus $2 per employee per month. This plan includes all features in Simple Start plan plus Manage and pay bills, and Instant sales and profit reports.
  • Plus – $159 /mo plus $2 per employee per month. This plan includes all features in essentials plan plus Track inventory and Manage 1099 contractors


Intuit Inc. Headquarters: 2700 Coast Ave, Mountain View, CA 94043, USA
Phone: 650-944-6000 Call Sales: 1.866.820.6377

Visit Quickbooks

Payroll Mate

Payroll Mate Payroll Software for Small Business

Payroll Mate is complete, stand-alone and desktop-based payroll software for accountants that does not rely on any third-party applications or systems to work. It offers users with solutions for payroll processing, benefits tracking, tax filing and compliance, and more.

Key Features

  • Automatically calculates federal and state payroll taxes – Payroll Mate automatically calculates net pay, federal withholding tax, Social Security tax, Medicare, state and local payroll taxes (all 50 states and District of Columbia). Tax tables and payroll formulas are updated throughout the year and pushed via the touch-free auto-update mechanism.
  • Multiple Pay Frequencies (Payroll Cycle Duration) – Payroll Mate supports different types of pay periods including weekly payroll, biweekly payroll, semimonthly payroll and monthly payroll.
  • Federal payroll forms – Payroll Mate supports the following federal quarterly and annual payroll forms (ready to sign and send): 941, 940, 943, 944, W-2 and W-3.
  • Multiple Pay Types – Payroll Mate supports regular salary, hourly pay, overtime pay, double overtime, bonus pay and commissions.
  • Vacation and sick time calculation and tracking – It tracks vacation and sick time off and adjusts the salary.
  • Direct Deposit – Prepares NACHA – ACH files for direct deposit payroll processing through a financial institution like a bank.
  • Print Checks – Prints signature ready checks and extensive pay stubs for your employees.
  • Customizable income, tax and deduction categories – This software also supports user-defined Income, Tax, and Pre-tax / Post-tax Deduction categories making it very flexible and powerful.
  • And more..

Integration with Accounting Software

General Ledger export feature inside Payroll Mate makes it open for working with most accounting applications that can import general ledger entries from file, such as Quickbooks, Sage 50, Quicken, Microsoft Accounting and more.

What are the system requirements for Payroll Mate?

Payroll Mate is Microsoft Windows compatible. For tablet users, Payroll Mate works on Microsoft Surface Pro and other devices that run fully functional Windows such as Dell Latitude and Toshiba Portege.


Payroll mate provides dedicated tutorials website with step by step instructions on how to use and customize the software. Users can browse and search for answers directly from inside Payroll Mate. It also offers friendly, helpful, professional and FREE US-based technical support by phone, email and chat.


Payroll Mate has costs $119 for the software. This license is valid for one calendar year for up to 10 companies and up to 75 employees per company. After the calendar year, users will have to pay another $119 to get a new software.


Office: 18313 Distinctive Drive – Orland Park, IL 60467, USA
1-800-507-1992 | 1-708-479-8731 | 1-708-590-6376

Visit Payroll Mate

2 thoughts on “Top 7 Payroll Software for Accountants

  • October 17, 2018 at 5:59 am

    Do these companies offer their products in India?


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