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5 Best Payroll Software for Accountants in 2025

Explore the 5 best payroll software for accountants in 2025. Compare features, accuracy, and efficiency to choose the ideal tool for managing payroll seamlessly.

Payroll Software for Accountants

What happens when accountants have to balance between regulatory changes and digital revolutions? In traditional accounting, accountants struggle to maintain efficiency and accuracy when handling large volumes of data. As technology keeps improving, accountants now have many payroll software options to choose from, but they still encounter some challenges along the way. Some of these challenges include difficulty in staying updated with regulations and managing income tax structures.

Payroll software helps businesses stay compliant with laws and avoid legal penalties. This listicle discusses the top 5 best payroll software for accountants, including their unique features and pricing models. It also states some of the key features of payroll software.

List of Best Payroll Software for Accountants

There are multiple options in payroll software available in the market for accountants. Below is the list of the top 5 best payroll software for accountants, including their features and price models for more understanding.

  1. factoHR
  2. greytHR
  3. Zoho Payroll
  4. Keka
  5. Quickbooks

1. factoHR

(4.7)
Overall
4.7
G2 Review
4.7
Google Play Store
4.1
Software Suggest
5.0
Customer Support
4.8
DIY Configuration
4.7

Features

factoHR’s mobile app allows employees to access personal information, like downloading payslips and tax forms. The software is configured to perform payroll processes with a formula-driven rule engine.
Processing of salaries with multiple payroll groups becomes easier with each payroll cycle. Organizations can stay updated on tax laws and maintain compliance with various rules.
Prevention of data duplication and effective data management become easier with a centralized management information system. The off-cycle payroll process helps organizations make additional payments, such as bonuses and incentives.
The custom report builder helps create tailored payroll reports and forms.
  • factoHR’s cloud-based solution includes strong security measures for remote access, allowing accountants to work from any location.
  • The software can automate salary calculations and necessary deductions related to taxes to help reduce manual errors.
  • It supports compliance with Indian labor laws and tax regulations, allowing accountants to stay updated with changing laws.
  • The software includes a step-by-step approach to payroll processing, helping accountants to minimize errors and simplify calculations.
  • Integration with popular accounting platforms, like Tally and SAP, is possible with factoHR for maintaining data consistency.
  • The software can help accountants by customizing and configuring salary structures to suit the needs of various clients.
  • With the ESS portal, employees can access salary details and tax forms without needing help from HR professionals.
  • Accountants can generate various payroll-related reports, for example, statutory compliance reports and year-to-date summaries, which are helpful for audit purposes.

Pricing

factoHR offers three pricing plans: Core, Premium, and Ultimate for up to 50 employees. The “Core” plan is ₹4,999 per month. The “Premium” plan is ₹5,999 per month. And the “Ultimate” is ₹6,999 per month.

Best Suited for

factoHR is suitable for small and medium-sized businesses. It is also highly suitable for large companies in various industries and sectors.

2. greytHR

Features

  • Statutory compliance
  • Automated reports and analytics
  • Cloud-based access
  • Intuitive and easy-to-use interface
  • Integration with accounting software, like Tally and Zoho Books

Pricing

greytHR’s pricing plans start with “Essential” at ₹3,495 per month for 50 employees. The “Growth” plan costs ₹5,495 per month for 50 employees. The “Enterprise” plan costs ₹7,495 per month for 50 employees.

Best Suited for

greytHR is best suited for small to large business enterprises.

3. Zoho Payroll

Features

  • Integration with Zoho Books
  • Collaboration tools to handle payroll-related tasks
  • Automates statutory compliance
  • Customizable reporting

Pricing

Zoho’s Payroll plans start with a “Standard” plan for ₹749 billed monthly. The “Professional” plan costs ₹1,499 per month. The “Premium” plan costs ₹2,999 per month. The “Elite” plan costs ₹4,999 per month.

Best Suited for

Zoho Payroll is best suited for small to medium-sized businesses.

4. Keka

Features

  • Automated payroll calculations
  • Easier bookkeeping and reporting
  • Compliance with local labor laws
  • Reporting & analytics
  • Accounting Integration with Tally and other software

Pricing

Keka’s plans start at “Foundation” for ₹9,999 per month, supporting up to 100 employees. The “Strength” plan costs ₹12,999 per month for 100 employees. The “Growth” plan costs ₹15,999 per month for 100 employees.

Best Suited for

Keka is well-suited for businesses of all sizes, from small to medium-sized enterprises (SMEs) to large enterprises.

5. QuickBooks

Features

  • Automated payroll runs
  • Automated tax calculations and filings
  • Direct deposit
  • Reporting and analytics

Pricing

QuickBooks’ pricing plan begins from “Simple Start” for $3.50 per month. The “Essential” plan costs $6.50 per month. The “Plus” plan costs $9.90 per month. The “Advanced” plan costs $23.50 per month.

Best Suited for

QuickBooks Payroll is best suited for small to medium-sized businesses.

What are the Must-Have Features for Accountants

When accountants select payroll software, certain key features need to be considered. The payroll software features help simplify payroll processes and maintain compliance with labor laws. Accountants require tools that can facilitate the calculation of salaries and tax deductions. There are some must-have features in payroll software that accountants need to manage payroll effectively.

Multi-Client or Multi-Company Management

Modern accounting firms and accountants consider multi-client or multi-company management as an important feature. In the traditional accounting method, accountants faced challenges in managing multiple clients and business entities. This software feature increases the quality of client service and efficiency.

TDS, EPF, ESI, and PT Automation

Automated systems help reduce the chance of manual errors in tax calculations. Businesses can avoid financial penalties or fines, as the software simplifies the payroll processes. The deductions, like Tax Deducted at Source (TDS) and Employee Provident Fund (EPF), are precise and comply with state and national laws. The software can automatically calculate Professional Tax (PT) and Employees’ State Insurance (ESI), along with other tax applicable brackets.

GST-Compliant Salary Structure Support

Businesses need to accurately calculate and report salaries to maintain payroll compliance with Goods and Services Tax (GST) laws. The software should be designed in accordance with GST laws to reduce the risk of errors. It should manage multiple salary structures according to GST regulations. It will help accountants save their time and focus on other strategic tasks, as the chances of errors are reduced.

Direct Salary Bank Transfers & E-Challans

When businesses offer direct deposit as a mode of payment, it eliminates the need for manual cheque writing. It saves time and reduces the risks of errors in payment distribution. It also reduces administrative costs for companies and the reconciliation efforts of accountants. E-challans allow taxpayers to make tax payments online through various methods, like net banking and credit cards. Taxpayers can check and use this functionality through the government’s official income tax website.

Customizable Reports and Payslips

When payroll software includes features like customizable payslips and reports, it allows flexibility in financial information for decision-making. This feature is also helpful for organizations conducting internal analysis and accountants conducting external assessments. Accountants can also generate specific reports while filing for the Income Tax Return (ITR). These automated report-generation features allow accountants to make informed decisions and improve the overall efficiency of the business.

Integration Capabilities

Integration capabilities are beneficial for accountants as they have access to real-time data from various systems. They can maintain accurate financial records and simplify the reconciliation process when data flow is easily accessible. Some payroll software provides built-in integration as a feature with platforms like Tally and Zoho Books. These systems sync payroll-related data in the company’s ledger and reduce the need for manual entry.

Form 16, Form 24Q, and Payroll Summaries

Form 16 is a TDS certificate issued annually by employers to employees, which shows the salaries paid and TDS deducted. Accountants have to make sure that the Form 16 generated is accurate and in accordance with income tax laws. Form 24Q is a quarterly TDS return that employers have to file to report TDS deducted from salaries. The payroll summaries help accountants reconcile payroll data and identify missing information before filing.

Bulk Salary Upload and Audit Trail

Bulk salary upload is a feature in some payroll software that allows accountants to process multiple salary payments in a single action. This method reduces manual and individual transactions, allowing them to reduce their administrative burden. Accountants can also save their time and focus on other higher-value tasks. An audit trail includes every bulk update and change made to records within the payroll system. Accountants can stay compliant with regulatory laws and retrieve the data whenever needed.

Conclusion

Payroll software for accountants has become a necessity for businesses that aim to stay compliant with various laws. When complex calculations and tax deductions are automated, efficiency can be improved in payroll management. The software suggests compliance updates and minimizes manual errors in payroll. As a result, businesses and accountants save time in automating routine administrative tasks.

The software can also help reduce the risk of financial penalties, as accountants can stay updated with national and regional laws. Organizations can enhance productivity, as the software can scale according to growing needs.

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