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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 | PF, ESIC, NPS, gratuity, and TDS processing |
| Geofenced and selfie-based attendance | Shift planning and roster management |
| Employee self-service portal (web and mobile) | Form 16 generation and e-filing support |
Pricing
- Core: ₹4,999/month (up to 50 employees), ₹69/additional employee/month. Billed quarterly.
- Premium: ₹5,999/month (up to 50 employees), ₹89/additional employee/month. Billed quarterly.
- Ultimate: ₹6,999/month (up to 50 employees), ₹119/additional employee/month. Billed quarterly.
- Offers customized plans for startups and blue-collar businesses.
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
- Maharashtra PT and statutory compliance automation
- Employee self-service portal with mobile app
Pricing
- Standard: ₹2995/month (up to 50 employees), ₹60/additional employee/month. Billed annually.
- Professional: ₹4495/month (up to 50 employees), ₹90/additional employee/month. Billed annually.
- Offers custom quotes for 100-plus employees under the Premium plan.
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 it handles basic payroll compliance. Growing businesses shift to paid plans for more advanced features like biometric integration.
Features
- One-click payroll
- PF, ESIC, TDS, and Form 16 generation
- Employee self-service portal and mobile app
- Payslip distribution via email and app
- Leave and attendance management with biometric support
- Free plan for up to 25 employees
Pricing
- Essential: ₹2,495/month (up to 50 employees), ₹45/additional employee/month.
- Growth: ₹4,495/month (up to 50 employees), ₹85/additional employee/month.
- Offers custom pricing under the Premium plan.
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
- PF, ESIC, PT, and TDS calculation
- Web-based HRMS and desktop payroll versions
- Attendance and leave management
- Full and final settlement processing
- Statutory filings and compliance reports
- Pune-based support and implementation
Pricing
- Rental Silver: ₹30 per credit.
- Rental Gold: ₹20 per credit.
- Rental Platinum: ₹10 per credit.
- Rental Diamond: ₹7 per credit.
- Rental Diamond Plus: On Demand.
- Outright Purchase Silver: ₹50000.
- Outright Purchase Gold: ₹75000.
- Outright Purchase Platinum: ₹100000.
- Outright Purchase Diamond: ₹150000.
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
- Payroll with PF, ESIC, PT, and TDS compliance
- Contract worker and shift tracking
- Leave and attendance management
- Employee self-service portal
- Recruitment and onboarding module
- Performance and appraisal management
Pricing
- Prime: ₹299/1 month (up to 10 employees), ₹30/additional employee, Max 40 employees.
- Plus: ₹449/1 month (up to 10 employees), ₹45/additional employee, Max 40 employees.
- Plus (Location Tracking): ₹499/12 months (up to 50 employees), ₹50/additional employee, Max 149 employees.
- Pro: ₹649/11 months (up to 10 employees), ₹60/additional employee, Max 500 employees.
- Ultra Biometric: ₹699/1 month (up to 100 employees), ₹50/additional employee, Max 500 employees.
- Offers Enterprise Pricing for more employees or custom features.
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
- End-to-end managed payroll processing
- Payslip generation and distribution
- Statutory filing and return submission
- HR advisory support
- 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
- Payroll processing with statutory compliance
- Attendance and leave tracking
- Employee self-service module
- Integration with CRM and business software
- Local Pune-based implementation and support
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
- End-to-end managed payroll processing
- Payroll audit and process review
- HR consulting and process advisory
- 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
- PF, ESIC, Maharashtra PT, and TDS compliance
- Multi-site gratuity calculation and tracking
- Shift and attendance management
- Employee self-service portal
- Recruitment and onboarding workflows
- Performance management and appraisal
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
- TDS, Form 16, and Form 24Q e-filing
- PF, ESIC, Maharashtra PT (MTR-6` challan), and LWF processing
- Attendance and leave management with biometric integration
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 |
Payroll Compliance Rules in Pune
Consider these payroll compliance rules for Pune when you configure your payroll policies.
Note: This list was last updated on 08/05/2026.
| Rule | Penalty |
|---|---|
Professional Tax:
|
Simple interest at 1.25%/month on overdue tax. Section 9. Non-payment after assessment: Section 10. Wilful evasion: Section 20. |
| Labour Welfare Fund: 5+ employees. Employee: ₹25; employer: ₹75 per employee per half-year. Section 6BB, Maharashtra LWF Act (Mah. XL of 1953), amended by Maharashtra Act 25 of 2024. Due June 30 and December 31. | Interest on overdue amounts after notice of demand. Section 6B. Obstruction or failure to produce documents: Section 17A. |
| Provident Fund: 20+ employees. 12% each. Due by the 15th. Code on Social Security, 2020, Chapter III. | 12% p.a. interest. EPF and MP Act, Section 7Q. Penal damages up to arrears. Section 14B. |
| ESIC: 10+ employees. Employer 3.25%, employee 0.75%. Ceiling ₹21,000/month. Due by the 15th. Code on Social Security, 2020, Chapter IV. | Deducted share not remitted: 1 to 3 years plus ₹1 lakh. Section 133(1)(i). Other defaults: 2 to 6 months plus ₹50,000. Section 133(1)(ii). |
| TDS on Salary: Deduct monthly. Remit by the 7th of the following month. File Form 24Q quarterly. Section 192, Income Tax Act, 1961. | Non deduction: 1%/month. Deducted but not remitted: 1.5%/month. Section 201(1A). Penalty equal to tax not deducted. Section 271C. Prosecution: 3 months to 7 years. Section 276B. |
| Bonus: 20+ employees. Salary ceiling ₹21,000/month. Minimum 8.33%, maximum 20%. Due within 8 months of the accounting year’s close. Payment of Bonus Act, 1965, Sections 10 and 11, subsumed under Code on Wages, 2019. | Imprisonment up to 6 months and/or fine up to ₹1,000. Section 28, Payment of Bonus Act, 1965. |
| Minimum Wages: Must pay at or above the Maharashtra-notified scheduled rate. Code on Wages, 2019, Section 6. | First offense: fine up to ₹50,000. Repeat within 5 years: up to 3 months imprisonment plus a fine of up to ₹1 lakh. Section 51, Code on Wages, 2019. |
| 50% Wage Rule: Basic wages must be at least 50% of CTC. Code on Wages, 2019, Section 2(y). Applies to PF computation under Section 2(88) of the Code on Social Security, 2020. | PF shortfall treated as arrears plus interest. Section 7Q and Section 14B, EPF and MP Act, 1952. |
| Gratuity: Payable after 5 years of continuous service. 15 days’ wages per completed year. Code on Social Security, 2020, Chapter V, Section 53. | False statement: up to 6 months and/or a fine of up to ₹10,000. Section 58(1). General contravention: 3 months to 1 year and/or ₹10,000 to ₹20,000. Section 58(2). Non-payment: 6 months to 2 years. Section 58(3). |
| Shops and Establishments: 20+ employees. Overtime beyond 10 hours/day or 48 hours/week is paid at twice the ordinary rate of wages. Total overtime not to exceed 144 hours per quarter. Section 12 (daily and weekly hours) and Section 15 (wages for overtime), Maharashtra Shops and Establishments (Regulation of Employment and Conditions of Service) Act, 2017 (Maharashtra 61 of 2017), as amended by Maharashtra Act 56 of 2025. | First offense: fine up to ₹1 lakh. continuing ₹2,000/day. Section 29(1). Repeat offense: fine up to ₹2 lakh. Section 29(2). Accident resulting in serious injury or death: 6 months imprisonment and a fine of ₹2 lakh to ₹5 lakh. Section 30. |
Why do You Need Payroll Software in Pune?
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 ull and final settlements to the mix, and payroll becomes the most time-consuming part of running a team in Pune.
factoHR Payroll Software 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 factoH R, 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.
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