Table of Contents
Managing payroll is difficult without payroll software in Pune. Even businesses using older systems need secure digital records and faster payroll processing. Frequent changes in state laws, such as the Maharashtra Shops Act, the MLWF (Maharashtra Labour Welfare Fund), and the new labour laws, necessitate the storage of digital records. Additionally, finance heads find it difficult to track and file tax reports due to frequent changes in professional tax rates.
Using cloud-based payroll management software in Pune simplifies payroll by automating deductions and securely storing records online. This guide helps HR heads and business owners compare features and pricing of the top 12 payroll software in Pune to choose a better solution.
Top 12 Payroll Software in Pune for 2026: Features, Pricing, and Best Fit for Your Business
Based on user reviews, features, and local support, factoHR, Pocket HRMS, Keka, Saral Pro, and IntelliPayroll are some of the top payroll software in Pune. First, we will discuss why these solutions are popular. Then, we will explore their features and pricing.
- factoHR: Great choice if you need to automate MLWF, professional tax, and Shops Act compliance.
- Pocket HRMS: Works well for teams that rely on field staff. Known for keeping PTEC and PTRC updated.
- Keka: Ideal for businesses that find full and final settlement difficult.
- Saral Pro: Recommended for its tax reports.
- greytHR: Ideal for mid-sized businesses.
- IntelliPayroll: A local brand for businesses that prefer Pune-based solutions.
- BizHRS: Best for manufacturing firms because of its shift rotation and overtime calculation.
- Talbuge: Best if you need local support in payroll and compliance.
- Horitech: Ideal for SMEs who want an easy-to-use solution.
- HR Remedy India: Perfect if you want a solution that takes care of local compliance.
- Ascent HCM: Popular choice for businesses that rely a lot on contractual employees.
- Sinewave Paywhiz: A tax-first tool that’s ideal for finance heads and accountants.
1. factoHR
factoHR is the best payroll software in Pune for teams that need support for complying with Maharashtra-specific regulations. HR managers value how it tracks MLWF, professional tax updates, and amendments to state and central regulations. Its geofenced attendance works well for hybrid workforces where attendance disputes delay payroll.
Features
| Maharashtra PT and MLWF calculation | Shift planning and roster management |
| Geofenced and selfie-based attendance | Form 16 generation and e-filing support |
| PF, ESIC, NPS, gratuity, and TDS processing | Employee self-service portal (web and mobile) |
Pricing
factoHR offers 3 plans starting at ₹4,999/month for up to 50 employees.
Best Suited for
Organizations of all sizes, including startups, mid-sized businesses, and large enterprises.
2. Pocket HRMS
Pocket HRMS is one of the leading payroll software providers in Pune that works well for IT services companies. Its geo-fenced attendance makes it easier for HR to track attendance, and its AI-powered chatbot makes sure that employees have all the answers to their payroll queries.
Features
- Custom payslip designer
- Old and new tax regimes support
- Geo-tagged and geo-fenced attendance
- AI chatbot (smHRty) for employee HR queries
- Employee self-service portal with mobile app
- Maharashtra PT and statutory compliance automation
Pricing
Pocket HRMS offers 3 plans starting at ₹2,995/month for up to 50 employees.
Best Suited
Growing companies in Pune with 50–500 employees.
3. Keka
Keka is a cloud-based payroll management software in Pune. It prevents state-specific compliance issues by tracking regulatory changes in Maharashtra, such as the revised 144-hour quarterly OT cap under the 2025 Shops Act amendment.
Features
- PF, ESIC, PT, and TDS compliance
- Payroll MIS reports and analytics
- Employee self-service portal and mobile app
- Leave and attendance with biometric integration
- Configurable salary structures and CTC components
- Shift management and OT tracking (144-hour quarterly cap)
Pricing
Keka offers customized plans based on your needs.
Best Suited
Mid-sized IT and product companies in Pune with 100–1,000 employees.
4. Saral Pro
Saral Pro is another payroll management software in Maharashtra that teams have relied on for years, because it handles PTRC and PTEC as distinct filings. Saral Pro can be bought with a licence, ideal for finance heads who prefer desktop software.
Features
- ESIC and LWF calculations
- PTRC and PTEC filing support
- Maharashtra PT (MTR-6 challan) processing
- XLS export and salary register in multiple formats
- Multi-company and branch support under one license
- PF ECR file generation and Form 24Q / Form 16 e-filing
Pricing
Pricing details available on request.
Best Suited
Small and mid-sized businesses in Pune that prefer licensed software.
5. greytHR
greytHR is another HR and payroll software in Pune that teams like. Its free plan is ideal for startups, as they can deduct PF, PT, ESI, and MLWF. Growing businesses shift to paid plans for more advanced features like biometric integration.
Features
- One-click payroll
- Free plan for up to 25 employees
- PF, ESIC, TDS, and Form 16 generation
- Payslip distribution via email and app
- Employee self-service portal and mobile app
- Leave and attendance management with biometric support
Pricing
greytHR is free for up to 25 employees; paid plans start at ₹3,495/month for up to 50 employees.
Best Suited
Startups and SMEs in Pune that are looking for payroll software with a free starter tier.
6. IntelliPayroll
IntelliPayroll is an affordable payroll software for startups in Pune, developed locally by Prodigy Technologies. With over a decade of experience in local payroll and compliance, it’s a perfect choice for businesses that prefer local support.
Features
- Attendance and leave management
- PF, ESIC, PT, and TDS calculation
- Full and final settlement processing
- Pune-based support and implementation
- Statutory filings and compliance reports
- Web-based HRMS and desktop payroll versions
Pricing
Pricing available on request.
Best Suited
Small and mid-sized businesses in Pune that want local payroll software.
7. BizHRS
BizHRS is a payroll management software in Pune that’s best for employers employing permanent and contractual employees. HR teams use it to track contract tenures against the 240-day rule (a threshold under the Industrial Disputes Act).
Features
- Employee self-service portal
- Leave and attendance management
- Recruitment and onboarding module
- Contract worker and shift tracking
- Performance and appraisal management
- Payroll with PF, ESIC, PT, and TDS compliance
Pricing
Pricing on request.
Best Suited
Small and mid-sized businesses in Pune.
8. Talbuge
Talbuge is among the payroll software companies in Pune that run payroll as a fully outsourced service. It handles processing, filings, and compliance for startups and mid-sized businesses. It is ideal for businesses that want to outsource their payroll, rather than managing payroll in-house.
Features
- HR advisory support
- Payslip generation and distribution
- End-to-end managed payroll processing
- Statutory filing and return submission
- Shops Act and LWF Form A/B register maintenance
- PF, ESIC, Maharashtra PT, and TDS compliance management
Pricing
Service-based pricing on request.
Best Suited
Small businesses and SMEs in Pune that want to outsource payroll.
9. Horitech
Horitech is a local payroll software company in Pune that offers payroll, CRM, and business management tools. It is ideal for small businesses that want a single platform for CRM, business intelligence, and payroll.
Features
- Attendance and leave tracking
- Employee self-service module
- Integration with CRM and business software
- Local Pune-based implementation and support
- Payroll processing with statutory compliance
Pricing
Pricing on request.
Best Suited
Small businesses in Pune that want payroll as part of a broader local software relationship.
10. HR Remedy India
If you are still working out how to choose payroll software in Pune or whether software is even the right fit, HR Remedy India manages payroll end-to-end for you. With regulatory changes such as Maharashtra’s proposed police verification requirement for gig and delivery workers, managing compliance has become more complex.
Features
- Payroll audit and process review
- HR consulting and process advisory
- End-to-end managed payroll processing
- Statutory filing and return submission
- Maharashtra PT, PF, ESIC, and TDS compliance
- Gig and contract worker compliance management
Pricing
Service-based pricing on request.
Best Suited
Pune-based businesses that prefer to outsource payroll and compliance.
11. Ascent HCM
Ascent HCM by Pune-based Eilisys Technologies is among the top payroll software companies in Pune for enterprises with operations across Pune and Thane. HR and finance heads use it to track gratuity eligibility under the unity of establishment doctrine.
Features
- Employee self-service portal
- Shift and attendance management
- Recruitment and onboarding workflows
- Performance management and appraisal
- Multi-site gratuity calculation and tracking
- PF, ESIC, Maharashtra PT, and TDS compliance
Pricing
Pricing on request.
Best Suited
Mid-to-large enterprises in Pune.
12. Sinewave Paywhiz
Sinewave’s Paywhiz is another leading payroll management software in Pune with 30+ years of operation and 30,000+ clients. Payroll teams in banking, BPO, and manufacturing use it for generating MTR-6 challan and complying with ESIC and PF.
Features
- ECR file generation for PF
- XLS import/export for salary data
- Attendance and leave management with biometric integration
- PF, ESIC, Maharashtra PT (MTR-6 challan), and LWF processing
- TDS, Form 16, and Form 24Q e-filing
Pricing
Pricing available on request.
Best Suited
Companies in banking, BPO, manufacturing, and education in Pune, as well as CA firms and payroll service providers.
We have also compiled a table of the best features in the top 12 payroll software in Pune that you can use to compare the available options.
| Software | Advanced Payroll Automation | Maharashtra PT Support | PF/ESIC/TDS Auto Compliance | Shift & Overtime Handling | Contract Labour Support | Employee Self Service (ESS) | Scalable for 50–1000+ Employees | Modern UI & Dashboard |
|---|---|---|---|---|---|---|---|---|
| factoHR | ||||||||
| Pocket HRMS | ||||||||
| Keka | ||||||||
| Saral Pro | ||||||||
| greytHR | ||||||||
| Intelli Payroll | ||||||||
| BizHRS | ||||||||
| Talbuge | ||||||||
| Horitech Payroll | ||||||||
| HR Remedy India | ||||||||
| Ascent HCM | ||||||||
| Sinewave |
Common Payroll Challenges for Businesses in Pune
There are seven challenges that companies face when managing payroll in Pune, including:
- Local compliance issues,
- Issues in processing payroll for large IT teams,
- Contract and outsourcing challenges,
- Salary delays and errors,
- Data security risks,
- Payroll issues with manufacturing firms, and
- Challenges faced by SMEs when managing payroll.
Now, let’s look at each challenge in detail and see how using payroll software in Pune can solve them.
Maharashtra Payroll Compliance Issues
The government amended the Shops Act in 2025 and raised the overtime cap to 144 hours per quarter. It also increased the minimum number of employees in a company to 20 workers. Maharashtra Labour Welfare Fund (MLWF) half-yearly contributions were also revised to ₹25 for employees and ₹75 for employers. PTRC and PTEC now require separate filings. Using payroll software in Pune helps you calculate and track all these deductions.
Payroll for Large IT Teams
Teams in Hinjewadi and Baner manage large hybrid workforces. In such a case, late or incomplete attendance reports make it difficult for HR to process salaries. Having a cloud-based payroll management software in Pune helps you avoid such scenarios by integrating attendance data with payroll.
Contract & Outsourced Payroll Challenges
Under the Industrial Disputes Act, completing 240 days of continuous service gives a contract worker eligibility for permanent employment rights. In February 2026, the Maharashtra government mandated police verification for gig workers. HR and payroll software in Pune helps set reminders and track verification status.
Salary Delays & Errors
The Wage Code sets a 48-hour window for full and final settlement. When payroll and attendance data exist in separate systems, this deadline becomes difficult to meet. Payroll management software in Pune keeps both in one place and reduces settlement delays and calculation errors.
Payroll Data Security Risks
Most businesses still run payroll on shared spreadsheets. These files contain PAN numbers, bank details, and salary information in one unprotected location. Payroll software in Pune secures this data using role-based access and encrypted storage.
Manufacturing Payroll Issues
Multi-shift operations in Chakan and Pimpri-Chinchwad require accurate overtime tracking. They must also maintain Labour Welfare Fund registers and determine ESIC eligibility. PF and ESI payroll software in Pune, built for shift operations, manages these requirements with automatic deductions.
SME Payroll Struggles
Crossing 20 workers makes Shops Act registration mandatory. It also triggers PTRC filings and MLWF contributions. An affordable payroll software for startups in Pune handles each statutory obligation based on state-specific rules.
Manage Payroll Smarter, Smoother & Faster with factoHR
Businesses find it difficult to keep up with PT slabs, MLWF contributions, PF, ESIC, and TDS. Add attendance disputes, late inputs, and full and final settlements to the mix, and payroll becomes the most time-consuming part of running a team in Pune.
factoHR brings all of it into one platform where compliance, attendance, and payroll are all managed together.
Compare it with your existing solution and see if factoHR provides what you need.
FAQs
How do I Choose the Right Payroll Software in Pune?
Compare the payroll management software offered by market leaders in Pune. Identify your sector and industry-specific needs, and make a decision.
What Features Should I Look for in Payroll Software?
Look for MLWF support, PT filings, Maharashtra Shops Act compliance, an AI-powered chatbot, and an ESS portal when you select any payroll management software in Pune.
Is there Affordable Payroll Software for Small Businesses in Pune?
Yes. Many software offer affordable plans, including factoHR. In fact, greytHR offers a free plan with limited features for up to 25 employees as well.
How Long does It Take to Implement Payroll Software?
Implementing payroll software takes somewhere around 4-12 weeks, which depends on company size and complexity. and custom needs. For Indian businesses with custom needs, the timelines can vary but fall under this range.
Which Payroll Software Supports Maharashtra PT Filing?
Most of the given software, such as factoHR, pocket HRMS, Keka, and Saral Pro, support PT filing in Pune.
What Kind of Businesses Need Payroll Software in Pune?
IT companies, manufacturing firms, startups, and even NGOs need to have payroll software in Pune due to complex payroll and compliance requirements.
© 2026 Copyright factoHR