7 Best Payroll Software for Accountants in [2024]

In today’s fast-paced business environment, accountants wear many hats. From managing complex financials to ensuring tax compliance, they have a demanding workload. One area that can eat into their valuable time is payroll processing.

This is where payroll software comes in. The right software can boost efficiency and save valuable time for accountants by automating calculations, ensuring accuracy, and simplifying tax filing.

But with so many available options, choosing the best fit for your business can be challenging.

This blog post aims to simplify your search process by exploring top payroll software solutions designed to meet the specific needs of accountants and CPA professionals.

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Which Accounting Software is Best for Payroll?

Here are some of the best accounting software that HR can use for payroll:



Paycor is a human capital management (HCM) software designed to simplify and automate payroll, HR, and workforce management tasks. It offers payroll, tax filing, compliance management, and workforce optimization solutions. It can be integrated with various applications, enabling seamless data sync and enhancing productivity.

Pricing: Paycor doesn’t have upfront pricing information. However, you can get a personalized quote from the sales team. The basic plan starts at $99.


  • Time Tracking: Helps approve time-off requests, Award PTO, and perform other time-tracking tasks.
  • Recruiting: Integrated dashboards for candidate tracking. You can establish custom hiring workflows for individual job roles.
  • Payroll: Contains must-have payment features, such as direct deposit, automatic payroll processing, and expense tracking capabilities.
  • Taxes: Helps you apply for tax credits and handle new hire filings. A financial dashboard consolidates all the data in one place.
  • Customization: This lets users create custom forms, calculations, views, and more.

Pros and Cons

Robust payroll management systemSlow customer service 
The setup process is simple Additional fees for dedicated support 
It is confusing to learn the use of reporting features 



Gusto is a full-service payroll and HR software for startups and small businesses. It handles payroll processing and benefits administration. Running regular payroll on Gusto is simple and flexible. It syncs with third-party software and can also be used as an integration.

It includes the choice of automated or manual payroll for employees and contractors, self-service profiles, tax filing, and time tracking.

Pricing: Starts at $40/month + $6/month per person for the simple plan.


  • Payroll: Gusto will run the payroll on schedule once an hourly rate or salary is set in an employee’s profile.
  • Integrations: It integrates with various accounting, time tracking, performance and expense management, and Point-of-Sale software applications. Some popular applications it can be integrated with are QuickBooks, Slack, Shopify, and Sage 50.
  • Hiring and Onboarding: Features like application tracking, background checks, offer letter templates, and onboarding checklists make the process quick and efficient.
  • Time Tracking: Available to plus and premium members, team members can clock in and out, and their work hours can be approved following this payroll, which is generated automatically.
  • Employee Self-Service Portal: Allows easy and fast self-onboarding for new employees. Once in the system, they can conveniently update all their essential information through the employee portal.

Pros and Cons

User-friendly interface Customization options are limited for lower-tier plans 
Flexible Payroll SchedulesLow scalability for larger-sized businesses 
HR tools for managing time off and compliance Additional fees for advanced features 



Workday is a Human Capital Management (HCM) tool that helps businesses manage multiple aspects of workforce management, including hiring, onboarding, time tracking, compensation, and reporting. It is an enterprise solution suitable for medium- to large-sized businesses.

Pricing: Workday gives a tailored quote based on the features required by the company. However, based on customer reviews, an estimated price is $99 per user per month.


  • Taxes: It can handle automatic payroll tax filings, saving the HR team time and energy while ensuring that taxes are accurate and timely.
  • Analytics: The analytics and reporting software provides managers with necessary insights on employee behavior and activities to facilitate informed and strategic decision-making about their workforce.
  • Customization: Workday can be customized in multiple ways. You can create personalized solutions based on your business needs and customize the dashboard.
  • Payroll: It ensures timely and accurate payments to all employees. You can update the general ledger when you run payroll, providing real-time visibility of your spending.
  • Recruiting: It is a powerful tool for sourcing, screening, and hiring candidates, offering you a centralized dashboard for talent acquisition and retention.

Pros and Cons

Strong product architecture Slow when multiple HR activities are running simultaneously 
It can be integrated with 600+ applications Long implementation time 
Cutting-edge talent management tools There is less room for user input  

Paychex Flex


Paychex Flex is an easy employee payroll platform for small businesses, in comparison to the more complex Paychex platform for larger businesses. It offers simplified payroll processing and tax filing for companies that don’t require a full suite of complex HR tools. Additional features like time tracking and benefits administration can be accessed from the Paychex platform.

Pricing: Starts at $39 per month, plus $5 per employee per month.


  • Compliance: All plans include new hire reporting for employees and contractors, ensuring reporting and tax filing meet state and local requirements.
  • Tax Filing: Calculation, payment, and filing of payroll taxes is done automatically for each pay period.
  • Voice Assist Capability: Allows hands-free payroll reviews, approvals, submissions, and updates. This improves the platform’s accessibility and promotes inclusivity for all employees.
  • Analytics and Reporting: It has custom analytics and reporting features.
  • Ease of Use: It strips down complex add-ons and features not required by small businesses, offering a simple payroll solution.

Pros and Cons

It is highly customizable  Pricing can be high for small business 
Strong HR and compliance features Slow customer support  
Voice Assist capability The learning curve for new users  

QuickBooks Payroll

quickbooks payroll

QuickBooks Payroll by Intuit is a payroll service with features like automated tax calculation, filing and payment for state and federal taxes, unlimited payroll runs, and benefits administration and reporting. It can be integrated with QuickBooks Accounting software, enabling users to manage accounting and payroll from the same platform.

Pricing: Starts at $45/month + $4 per employee


  • Ease of Use: Payroll data, list of banks, next payroll run date, and more can be accessed from a single dashboard. Adding and updating are extremely simple.
  • Tax Filing: Relevant tax forms are generated automatically. It calculates, files, and pays all federal and state payrolls.
  • Time Tracking: Included in the Premium and Elite models, QuickBooks Time is a time-tracking app by Intuit.
  • Analytics and Reporting: Customize reports and dashboards at your convenience. It includes reports such as payroll billing summary, payroll deductions and contributions, payroll tax liability, and more.
  • Benefits Administration: Enables you to offer competitive benefits to your employees.

Pros and Cons

User-friendly interface Limited features in low-tier plans 
Seamless integration with different QuickBooks versions More expensive than most leading competitors 
Good, customizable reports Customer support is slow and unresponsive 



A reliable payroll service provider, the SurePayroll platform includes seamless payroll processing, tax services, and compliance management. It is ideal for small businesses that want to pay their employees with an easy-to-use and affordable system. It also handles tax-related tasks, payments, and filings on behalf of companies.

Pricing: Starts at $19.99/month + $4/employee per month.


  • Direct Deposit: SurePayroll automatically transfers employee net pay to their designated bank accounts on payday.
  • Analytics and Reporting: It provides payroll reports like payroll summary, taxable wages, check registry, and more that maintain transparency and provide valuable insights.
  • Employee Management and PTO: Managing employees and time off is straightforward and customizable.
  • Accounting Integration: Easily import data into your general ledger by integrating with accounting systems like QuickBooks Desktop & Online, Xero, AccountEdge, and Sage 50.
  • Auto Payroll: Set up auto payroll by entering wage information and pay schedules. It can be used for both hourly and salaried employees.

Pros and Cons

Good tax support Tax filing is only included in the full-service pan  
Affordable plans compared to competitors There is no built-in time tracking 
Simplified automated payroll and tax filing The advanced needs of growing businesses may not be supported 



OnPay is one of the top payroll software applications for small businesses. An easy-to-navigate and well-designed dashboard offers a simple and streamlined method to run payroll for a small business. It includes various HR tools like new hire reporting, custom checklists, and an HR resource library.

Pricing: Starts at $40/month + $6/employee per month.


  • Payroll: Access unlimited payroll runs and enable various pay schedules and rates for part-time, full-time, and contract workers.
  • Onboarding: Self-onboarding for new employees saves you time and hassle. Employees can fill in essential details like their banking information that the employer requires to pay them.
  • Tax Filing: OnPay automates much of the tax process. Tax documents are available to employees in the portal. It files taxes for your company after deducting what’s necessary at the end of the tax year.
  • Benefits administration: A visually appealing dashboard is present for admins to keep track of employees who’ve finished, started, or not yet started their benefits elections. Employers can choose health insurance benefits for their employees and integrate them with their payroll.
  • Integrations: OnPay can be integrated with numerous accounting, time tracking, HR compliance, and 401(k) management applications like QuickBooks Desktop, QuickBooks Time, Vestwell, Magnify, Xero, and more.

Pros and Cons

Unlimited payroll runs The time tracking feature is not inbuilt 
Self-service employee portal Mailing tax documents costs extra  
Offers extensive HR resources portal The mobile application is available only for iOS users. 


Before you hit the purchase button, consider your business needs. Some of the factors to keep in mind are:

By carefully considering your requirements, you can find a payroll solution that streamlines your workflow and improves productivity.

What’s more? Hosting your payroll software on the cloud with a managed hosting provider such as Ace Cloud can help you with remote access to the applications along with secure and reliable infrastructure to run your business online. Cloud-hosted payroll software will simplify operations, ensure reduced costs, and improve accessibility to data.

Which payroll software are you using for your business? Please share in the comment section below.

About Julie Watson

Julie is a dynamic professional with over 16 years of rich experience as a VDI and Application Hosting expert. At Ace Cloud Hosting, she humanizes disruptive and emerging remote working trends to help leaders discover new and better possibilities for digital transformation and innovation by using cloud solutions with an enterprise-class security approach. Beyond work, Julie is a passionate surfer.
On the weekend, you will find her hanging out with her family or surfing around the North Shore of Oahu.

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