Payroll Software For Accountants

by Navicasoft
27 Vendors Reviewed
34 Hours of Research
25 Experts Interviewed

Payroll is a difficult task for any company and requires continuous maintenance to ensure compliance with all regulations, which change over time. Payroll software is an invaluable addition to the HR department and streamlines all the tasks involved in managing payroll. 

It eliminates the need for tedious calculations, assistance from other departments, and potential payroll mistakes such as rates or taxes incorrectly calculated by employees.

Payroll Software For Accountants

The chosen system will depend on your requirements, such as whether you are in the US or not, whether you need a cloud-based model, how many employees there are, what kind of tax rates you have, etc. Below you can find the list of best payroll software for accountants available on the market with its pros and cons.

Our Top 5 Payroll Software For Accountants

Payroll Software For Accountants Reviews

1. Best Overall: QuickBooks Online Payroll

QuickBooks Online Payroll QuickBooks Online Payroll logo

Our rating: ★★★★★

If you’re an accountant and you’ve been using QuickBooks Desktop, you’ll be delighted to know that there is a solution for your payroll processing woes. QuickBooks Online Payroll allows thousands of accountants to process their clients’ payroll information in their existing QuickBooks environment without having the added expense of purchasing the software. 

QuickBooks Online Payroll Review

QuickBooks Online Payroll has a wide variety of features that accountants will appreciate. Besides providing an easy way to import clients’ information from QuickBooks, this service allows accountants to process all their payroll data in one place, saving them time and money. By creating a Professional Services Agreement or creating a subscription service with QuickBooks online payroll, you can take advantage of some features that aren’t available at no cost.

Pricing Plans

  • Core – $22.50 per month.
  • Premium – $37.50 per month.
  • Elite – $62.50 per month.

All Plans Include

  • Numerous payroll features.
  • Automated taxes and forms.
  • 401(k) plans.
  • 1099 E-File & Pay.
  • Expert product support.
  • Workers’ comp administration.
  • 24/7 expert support.
  • Tax Penalty Protection.

2. Best For Nonprofit: Sage Intacct

Sage Intacct Sage Intacct logo

Our rating: ★★★★★

Sage Intacct is a cloud-based payroll software that has a variety of features. The product can be used by business owners, accountants, bookkeepers, and managers. It’s designed to manage the entire company from accounting to payroll and HR management.

The system also offers customizable features, so you can add or remove what works best for you. Sage Intacct also provides email reports that are easy to read and includes charts for important data analysis on your business finances.

Sage Intacct Review

On the site, users can manage their employees and clients using their Sage Intacct software. You can view an employee’s salary, tips, commissions, and more. It also allows management to see employee expenses and payouts, track risks, maintenance requests, and compliance reporting.

Each user has a customized dashboard that displays the company’s financial information; it consists of six panes: sales summary, cash totals, cash flow forecast, bank account summary, sales credit card details, and compensation plan details. The tools allow you to make changes in your accounting system as necessary or adjust payroll for a specific client or employee.

All Plans Include

  • Payroll.
  • Tax reporting.
  • Calendar, time & attendance tracking.
  • Customer support.

3. Best For Automate Payroll Taxes: Gusto

Gusto Gusto logo

Our rating: ★★★★★

Gusto is a payroll software for accountants that’s compatible with the new US tax code. We provide exponential growth for small businesses and accountants. Don’t miss out on this opportunity to start your company on the right foot and free up your time from office work!

Gusto Revview

The features you can expect from Gusto are as follows: 

Easy Payments

With just one click, your client will be able to pay their bills. 

Simple Pricing

Their pricing is structured in tiers and includes a lot of flexibility for accounting firms, meaning more consistency in your rates and happier clients. 

Payment Integration System

They bring together all your transactions into one easy-to-access tool, so you don’t have to hunt down each payment record anymore.

Pricing Plans

  • Core – $6/mo per person, plus $39/mo base price.
  • Complete – $12/mo per person, plus $39/mo base price.
  • Concierge – $12/mo per person, plus $149/mo base price.
  • Contractor – $6/mo per person, plus $0/mo base price.

All Plans Include

  • Full-service payroll across all 50 states.
  • Employee self-service and profiles.
  • Next-day direct deposit.
  • Dedicated best-in-class support.
  • Customizable employee onboarding tools.
  • Accounting and time tracking integrations.
  • Project tracking and workforce costing.
  • Certified HR pros.

4. Best For Small Business: Onpay

Onpay Onpay logo

Our rating: ★★★★★

Onpay is a payroll software for accountants that provides users with powerful features at an affordable price. Onpay was created to make payroll processing quicker and easier for accountants so their clients could focus on the more important business matters of the day. With many features and our integration with QuickBooks, you won’t have to worry about keeping up with all of your clients’ data.

Onpay Review

Onpay is a powerful payroll software package that comes with the ability to offer each customer an invoice, invoice reminders, client dashboard, reports for various accounting software features such as hours worked for each employee, and time-off requests. 

This software saves hours that would otherwise be wasted on tedious tasks. What’s more, is that it gives users the ability to customize their invoices with unique letterheads and logos so your clients can see who they’re working with.

All Plans Include

  • Full-service payroll.
  • Unlimited monthly pay runs.
  • All tax filings and payments.
  • W-2 and 1099 workers.
  • Pay by direct deposit, debit card, or check.
  • Multiple pay rates and schedules.
  • Multi-state payroll.

5. Best Reporting: Paychex Flex

Paychex Flex Paychex Flex logo

Our rating: ★★★★★

Paychex Flex is online software that aids accountants in managing their payroll more efficiently. Employers can also use it to provide online access for payroll services for an organization, including invoicing, review of paystubs, and over-the-counter payments.

Paychex Flex Review

Paychex Flex software provides the following features:

  • Simplified interface, which makes it easy to use.
  • Quick Pay feature allows employees to make payments directly from their checking or savings accounts without creating or downloading checks.
  • Support around the clock for any type of question you may have regarding the service.

Paychex Flex is helpful to: 

  • Accountants and bookkeepers.
  • Businesses that want to provide online payroll services for employees.

The Paychex Flex service saves time and money; it is an easy-to-use tool that automates the payroll process, which allows employee payments to be processed quicker. This improves efficiency and reduces unnecessary costs. The Paychex Flex software also gives employees access to their pay stubs, allowing them to set up direct deposits easily while also reducing the need for printing checks.

Buyer’s Guide

While choosing the payroll software for accountants, first of all, you need to consider how the software you are going to buy will be used, by whom, and for what purposes. Every employee is different, and you cannot expect that one single type of interface will be conducive for them all. 

Payroll Software For Accountants Buyer’s Guide

The interface needs to be simple yet professional and easy to use. You need to see if it is compatible with the devices your employees already have. The support provided by the vendor is also very important because it will let you know how fast they respond when it comes to solving issues, whether there are any bugs or issues with the software or not, and whether they provide helpful tips that can make your work easier.

What Is Payroll Software For Accountants?

Payroll software is a program that helps to manage the payroll of employees of a company. It includes several features which allow you to achieve this objective, and it is the most common application today, being used by most companies worldwide. 

What Is Payroll Software For Accountants

Such types of software allow you to calculate wages, taxes for employees, withholdings for the government, insurance payments, and more. Depending on the software model you use, it can calculate taxes such as income tax or VAT and payroll tax. Some models include plans for some other tax types, such as business tax or insurance for some states in the US.

Benefits Of Payroll Software For Accountants

A payroll software solution allows you to improve your company’s profitability by reducing payroll costs. You will save money on time spent by calculating payroll, as it will be done automatically by the software. An automated system will also calculate payroll taxes and deductions for different benefits provided to employees, such as health insurance, retirement plans, or other payments that you agree with your employees.

Benefits Of Payroll Software For Accountants

Improving productivity can be very helpful for every business, as it goes directly into profitability. You can quickly identify your employees’ earnings if you have a standard number such as $100 a day or week, which each employee is supposed to receive depending on their position and skills required for the job they have. Payroll software will calculate this average number as well as the monthly earnings. It will also calculate all possible deductions depending on the number of days worked per month plus one day.

Another benefit of payroll software is that you will easily update your knowledge about all applicable regulations and tax codes. This can be very crucial in today’s world, where technology evolves at an incredible speed. You can use web-based solutions for all your payroll needs accessible from any computer connected to your network.

Payroll Software For Accountants Deployment

When you choose payroll software for your business, you need to decide whether to use it online or a local solution. If you decide on the first option, you can purchase a cloud-based model installed in different companies and is accessible from anywhere where there is an internet connection. The other option is to install the program on your computer to make it accessible to employees and administrators.

How To Choose Payroll Software For Accountants?

Many accountants are turning to payroll software, but it’s a complicated decision. It can be challenging to choose the right software for your business. You’ll need to factor in such things as what kind of features and integrations you require, your budget, and the time it will take you to learn the terminology.

How To Choose Payroll Software For Accountants

Here’re other things to consider while choosing such kind of software:

  • First, make sure you can find accounting software that is compatible with your operating system
  • Second, see if the software suite offers any training or educational courses to help you learn the program
  • Third, ask yourself how much of your time will be taken up by answering questions and what steps need to be followed before paychecks are distributed 

Finally, consider whether or not this software will be worth the investment for you and your company. Can it save you money? Is there a reasonable cost for it? Will it improve efficiency? Keep in mind that choosing payroll software is very important to review these steps when considering options.


What Is The Best Software For Payroll?

The two most popular software providers for payroll are QuickBooks and Sage 50. The difference between the two is QuickBooks has a one-time purchase price, whereas Sage 50 requires a monthly fee that includes support. Both of them offer accessible, user-friendly interfaces, but it’s hard to say which one is better as both of them are excellent in their own way.

How Does Payroll Software Work?

Here’s our quick explanation of how payroll works. In order to pay employees, you need to calculate how much they have earned. For example, in a month where the employee has worked 10 hours per day for 30 days, their gross earnings are $600 ($10 x 3 hours x 10 days). Now it’s time to deduct taxes and other withholdings. In the United States, these include federal income tax, state income tax, and Social Security contribution.

Is QuickBooks Good For Accountants?

Yes. QuickBooks is accounting software that handles many accountants’ work, like creating bills and invoices, not just report numbers. It can also handle payroll functions with its payroll module. Accountants are constantly dealing with clients about their QuickBooks account balances, so they use it often in their jobs.

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