7 Best Payroll Apps With Overtime & Deduction Management in India for 2026

Managing payroll efficiently is crucial for Indian businesses, especially with evolving labour laws, complex tax deductions like TDS, and statutory contributions such as Provident Fund (PF) and ESI. In 2026, payroll challenges include ensuring statutory compliance, accurate overtime calculations, seamless deduction management, and timely pay slip generation while minimizing compliance risks and human errors.

The right payroll software or HR payroll software can transform these tasks through payroll automation, integrating attendance tracking, leave management, and employee self-service portals. This not only ensures tax accuracy and on-time payments but also boosts business efficiency, employee satisfaction, and employee retention.

Why Payroll Automation Matters for Indian Businesses

Manual payroll processing often leads to errors in salary calculations, overlooked tax deductions, or delayed compliance filings, resulting in penalties. Modern payroll apps automate salary calculations, handle statutory deductions (PF, ESI, Professional Tax, TDS), manage overtime calculations, and generate statutory reports effortlessly.

Key benefits include:

• Streamlined payroll processing with reduced compliance risks.
• Integration with time tracking tools, biometric attendance, and HRIS for accurate inputs.
• Employee self-service features like mobile access to payslips, tax projections, and investment declarations.
• Scalability for startups, SMEs, and enterprises, supporting multi-location operations and multi-state compliance.
• Advanced features like reimbursements, flexi-benefits, arrears calculations, and full and final settlement.

Choosing the best payroll app depends on your business size, industry needs, budget, and requirements for customization, reporting and analytics, and data security.

Key Features to Look for in Payroll Apps

When evaluating payroll management software, prioritize:

• Automates salary calculations including bonuses, overtime, and deductions.
• Full statutory compliance with PF, ESI, TDS, PT, and LWF.
• Overtime & deduction management with flexible rules.
• Payslip generation and direct bank transfers.
• Attendance tracking (GPS, biometric) and leave management.
• Employee self-service portal for transparency.
• Reporting and analytics for insights into payroll costs.
• Integration capabilities with accounting tools, HR systems, and time tracking.
• Mobile-first experience for on-the-go access.
• Data encryption and audit trails for security.

Now, let’s dive into the 7 best payroll apps with strong overtime & deduction management capabilities.

1. Salarybox

Salarybox stands out as a top payroll app in India, particularly for startups and SMEs. It’s a mobile-first payroll automation software designed for ease of use, with seamless integration of attendance tracking via GPS and biometric devices. It excels in automating payroll processes, handling overtime calculations, and managing deductions accurately while ensuring full compliance with Indian labour laws.

Pros:

• Highly user-friendly interface with a strong mobile app for both admins and employees.
• Excellent attendance tracking with GPS-based attendance and real-time insights.
• Fast and accurate payroll processing, including overtime calculations and statutory deductions (PF, ESI, TDS).
• Affordable pricing and great value for small teams.
• Strong customer support and quick issue resolution.
• Features like employee self-service, payslip generation, and reimbursements enhance employee experience.

Cons:

• Advanced customization for very complex enterprise needs may require additional setup, which allows for tailored growth as your business scales.

2. greytHR

greytHR is a comprehensive HR payroll software trusted by thousands of Indian businesses. It offers robust payroll management with deep integration for attendance, leave, and compliance.

Pros:

• Thorough statutory compliance handling PF, ESI, TDS, and more with automated filings.
• Excellent for mid-sized companies with configurable workflows.
• Strong reporting and analytics capabilities.
• Integrates well with biometric devices.
• Reliable support and regular updates.

Cons:

• Interfaces can feel dated compared to newer mobile-first apps.
• Mobile apps lack some desktop features and may have occasional performance issues.

3. RazorpayX Payroll

RazorpayX Payroll leverages fintech strengths for seamless payroll processing and disbursements, making it ideal for businesses prioritizing quick payments.

Pros:

• Automated compliance and direct bank integrations for fast salary disbursements.
• User-friendly for basic payroll needs with employee self-service.
• Handles reimbursements and contractor payments efficiently.
• WhatsApp integration for payslips.

Cons:

• Limited advanced HR features like deep attendance or performance management.
• Customization options are somewhat restricted.
• Can feel expensive for very small teams.

4. Zoho Payroll

Part of the Zoho ecosystem, Zoho Payroll focuses on simple, compliant payroll for Indian businesses with seamless integrations.

Pros:

• Easy automation of salary calculations, deductions, and payslips.
• Strong compliance with Indian tax laws.
• Integrates natively with other Zoho tools like Books and People.
• Affordable and straightforward for small teams.

Cons:

• Limited to India (and a few regions); lacks global/multi-country depth.
• Minimal advanced features like native time tracking or complex overtime rules.
• Reporting customization is basic.

5. Keka

Keka is an employee-centric HRMS with powerful payroll capabilities, popular for its modern interface and automation.

Pros:

• Intuitive UI with strong payroll automation and compliance.
• Excellent attendance and leave sync for accurate overtime and deductions.
• Performance management integration.
• Good for growing teams with scalable features.

Cons:

• Can have occasional glitches in mobile app or payroll accuracy.
• Learning curve for advanced features.
• Support response times vary.

6. Pocket HRMS

Pocket HRMS is an AI-powered solution offering end-to-end HR and payroll for Indian businesses.

Pros:

• Automated payroll with machine learning for anomaly detection.
• Strong compliance and customizable salary structures.
• Mobile app and chatbot for employee queries.
• Good for multi-location operations.

Cons:

• Interface navigation can be confusing initially.
• Some users report slow support TAT.

7. Zimyo

Zimyo is a unified HRMS platform with solid payroll features, focusing on efficiency and analytics.

Pros:

• Affordable with good integration capabilities.
• Automated payroll and compliance for PF, ESI, TDS.
• Real-time dashboards and employee engagement tools.
• Scalable for SMEs.

Cons:

• The platform can be slow at times.
• UI complexity and setup may require support.

How to Choose the Right Payroll App for Your Business

Consider your business size (startups vs. enterprises), growth potential, pricing structures, and need for integrations. Prioritize ROI through time-saving automation, cost savings on errors/penalties, and improved employee satisfaction.

For small businesses and startups, mobile-first apps like Salarybox offer quick wins. Larger teams may prefer comprehensive platforms like SalaryBox.

FAQs

1. What is the best payroll software for small businesses in India?

Apps like Salarybox are ideal for small teams due to their affordability, ease of use, and mobile access.

2. How do these apps handle overtime calculations and deductions?

Most automate overtime based on attendance inputs and apply rules for deductions like PF (12%), ESI, and TDS slabs accurately.

3. Are these payroll apps compliant with Indian labour laws?

Yes, top ones automatically update for PF, ESI, TDS, PT, and generate forms like Form 16.

4. Can payroll software integrate with attendance tracking?

Absolutely, many support biometric, GPS, and time clock tools for seamless overtime and leave adjustments.

5. What about data security in payroll apps?

Reputable apps use encryption, audit trails, and role-based access to protect sensitive data.

6. Is there a free payroll software option?

Some offer free trials or limited plans, but paid versions provide full compliance and features.

7. How does payroll automation save time?

It reduces manual calculations, errors, and filings, often cutting processing time by 70-80%.

Investing in the right payroll app like SalaryBox ensures operational efficiency, legal compliance, and happier employees in 2026.