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Payroll Services in Pune: CA-Managed Salary Processing and Compliance

Reviewed by CA and CS Team, Patron Accounting LLP ICAI & ICSI Registered| 15+ Years Experience| Last Updated: 13 March 2026 Verify Credentials →

Documents: Employee master data, PAN, Aadhaar, bank details, salary structure, attendance records

Fees: Starting from Rs 1,499/month (up to 10 employees, all statutory compliances included)

Eligibility: All employers - IT companies, manufacturers, startups, MSMEs in Pune

Timeline: Payroll setup in 3-5 working days; salary processing by 1st of every month

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Outstanding payroll compliance. Patron handled EPF, ESIC, and Form 16 for our Hinjewadi IT team seamlessly.
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Patron has helped 10,000+ businesses with payroll processing, EPF/ESIC compliance, and Form 16 delivery. Pune employers trust us for CA-managed payroll with zero late filing penalties.

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Payroll Services in Pune - Overview

📌 TL;DR - Payroll Services in Pune Services at a Glance

Payroll services cover end-to-end salary processing, statutory deductions (EPF, ESIC, TDS, PT), compliance filing, and employee payslip generation. Every employer with 20+ employees must register under EPF; those with 10+ employees earning up to Rs 21,000/month under ESIC. Under the Code on Wages (effective Nov 2025), basic pay must be at least 50% of CTC - directly increasing EPF/ESIC bases for Pune employers.

Pune employs over 2 million people across IT parks in Hinjewadi and Kharadi, automotive plants in Chakan, and manufacturing units in MIDC Bhosari. Every employer must process salaries accurately, deduct contributions on time, and file monthly returns. Learn more about Payroll Services across India.

Maharashtra PT Act 1975 adds another layer - PTRC is mandatory for every employer. The Income Tax Act 2025 (effective 1 April 2026) introduces revised TDS rules. Patron Accounting manages payroll from our Pune office at RTC Silver, Wagholi - handling salary processing, EPF/ESIC/PT/TDS compliance, Form 16, and integration with Accounting Services and Zoho Books.

Content is reviewed quarterly for accuracy.

What Are Payroll Services?

Payroll services refer to the end-to-end management of employee salary processing, statutory deductions, compliance filings, and payslip generation for businesses, governed by the EPF Act 1952, the ESI Act 1948, and the Income Tax Act.

For Pune's IT sector - companies in Hinjewadi employing thousands with complex salary structures - accurate payroll is critical. A single EPF calculation error triggers penalty notices under Section 14B with damages from 5% to 100% of arrears. When managed by a CA firm, payroll integrates with TDS compliance, Form 16, statutory audit, and complete books of account maintenance.

Coordination with the Regional PF Commissioner, Pune and EPFO portal, ESIC Regional Office, Pune, and Maharashtra GST Department for PTRC ensures your Pune business meets every statutory deadline without penalty risk.

Key Terms for Payroll Services in Pune:

EPF: 12% employee + 12% employer on basic + DA. Mandatory for 20+ employees. Deposit by 15th. Section 14B damages for late payment.

ESIC: 0.75% employee + 3.25% employer for salary up to Rs 21,000/month. 10+ employees in Maharashtra.

Code on Wages 2019: Basic pay must be at least 50% of CTC (effective Nov 2025). Increases EPF/ESIC contribution bases.

Maharashtra PT Act 1975: PTRC for employers, PTEC for entities. Male threshold Rs 7,500/month. Max Rs 2,500/year.

Form 24Q: Quarterly TDS return for salary deductions filed with Income Tax Department.

Section 14B: EPF penalty for late deposit - 5% to 100% of arrears depending on delay period.

APL-05 Payroll Services in Pune
Pune Payroll Hub Compliant

Who Needs Payroll Services in Pune?

IT Companies (Hinjewadi, Kharadi, Magarpatta): Large engineering teams with variable compensation. EPF mandatory for 20+ employees. ESIC for salary up to Rs 21,000. Complex TDS with old/new regime choices. Bundle with GST Registration in Pune.

Manufacturers (Chakan, MIDC Bhosari): Permanent, contract, and temporary workers across shifts. Payment of Wages Act: salary by 7th/10th. Factories Act overtime at 2x wage rate. EPF on basic + DA.

Startups (Magarpatta, Baner): Cross 10/20-employee thresholds during growth. Early EPF/ESIC registration prevents backdated liabilities. Code on Wages: 50% basic of CTC impacts PF calculations.

Professional Services (Koregaon Park, Wakad, Viman Nagar): Small-mid teams where each employee's tax regime choice (old vs new Section 115BAC) affects TDS computation. Investment proof verification during Jan-Mar.

Contract Labour Employers: Principal employer liable for contractor default under Contract Labour Act 1970. Separate compliance reports per contractor required.

Payroll Services Included by Patron in Pune

ServiceWhat We Do
Salary ProcessingMonthly computation: basic, HRA, allowances, incentives, overtime, arrears. Bank advice file for bulk transfer across Pune bank branches
EPF Administration12%+12% calculation, ECR generation, EPFO portal filing, UAN activation, Aadhaar-KYC linking. Coordination with Regional PF Commissioner, Pune
ESIC Compliance0.75%+3.25% calculation for employees up to Rs 21,000/month. Monthly challan, IP number generation, half-yearly returns with ESIC Regional Office, Pune
TDS on Salary (Section 192)Monthly TDS per declared regime and investments. Quarterly Form 24Q filing. Annual Form 16 by 15 June. TDS deposit by 7th
Maharashtra PT (PTRC/PTEC)Monthly PT deduction per Maharashtra PT Act 1975 slabs. PTRC return on mahagst.gov.in. PTEC payment tracking. Due 15 March 2026 for FY 2025-26
Maharashtra LWFEmployer Rs 12 + Employee Rs 6. June and December contribution periods under LWF Act 1953
Full and Final SettlementSeparation salary, leave encashment, bonus pro-rata, gratuity (5+ years under Payment of Gratuity Act 1972), PF transfer guidance
Statutory Audit SupportYear-end reconciliation with books, EPF/ESIC certificates, PT receipts, TDS computation sheets for statutory auditor
Our Process

How Payroll Services Work in Pune - 6-Step Process

Patron manages the complete payroll cycle - from onboarding to annual compliance and statutory audit support.

Step 1

Onboard and Configure Payroll

Collect employee master data (PAN, Aadhaar, bank, salary structure). Register with Regional PF Commissioner Pune (20+ employees) and ESIC Regional Office Pune. PTRC on mahagst.gov.in. Configure CTC with basic pay at 50% per Code on Wages.

EPF/ESIC Registered PTRC Setup
Onboarded01
Step 2

Collect Monthly Attendance and Inputs

Attendance, leave records, overtime (Chakan manufacturing under Factories Act), new joiners, separations, salary revisions, reimbursements. IT companies: variable pay, project bonuses, stock option perquisite valuations.

Attendance Inputs Received
Data Ready02
Step 3

Compute Salary and Statutory Deductions

Gross salary, EPF (12%+12% of basic+DA), ESIC (0.75%+3.25% for eligible), TDS Section 192 per regime and investments, Maharashtra PT per slab, LWF (June/December). Net salary computed after all deductions.

Computed Deductions Applied
Salary Ready03
Step 4

Process Payment and File Returns

Bank advice for bulk salary transfer. EPF ECR on EPFO Unified Portal. ESIC challan by 15th. TDS deposit by 7th under Section 194. PTRC return on mahagst.gov.in by last day of month (monthly) or 31 March (annual). FY 2025-26 revised due: 15 March 2026.

Salary Paid Returns Filed
Processed04
Step 5

Generate Payslips and Compliance Reports

Digital payslips with CTC breakdown distributed to employees. Monthly reports: EPF contribution summary, ESIC eligibility tracker, TDS computation sheet, PT deduction register. For manufacturers with contract labour: separate reports per contractor.

Payslips Sent MIS Reports
Reports Done05
Step 6

File Quarterly Returns and Annual Compliance

Form 24Q quarterly. Annual PF reconciliation. ESIC half-yearly returns. Form 16 by 15 June. Year-end payroll reconciliation for statutory audit ensuring P&L salary expense matches EPF/ESIC/TDS records. Gratuity provision computed under Payment of Gratuity Act 1972.

Form 16 Done Audit Ready
Cycle Complete06

Documents Required for Payroll Setup in Pune

  • Company PAN Card and Certificate of Incorporation / Partnership Deed
  • EPF registration certificate (if already registered with Regional PF Commissioner, Pune)
  • ESIC registration certificate (if already registered with ESIC Regional Office, Pune)
  • PTRC certificate from Maharashtra GST Department (mahagst.gov.in)
  • Maharashtra Shops & Establishments registration certificate
  • Employee master list with PAN, Aadhaar, bank account details, and date of joining
  • CTC structure and salary breakup for each employee
  • Attendance and leave policy document
  • Previous months' payroll data (if migrating from another provider)
  • TAN (Tax Deduction Account Number) for TDS compliance

Pune-specific tip: Manufacturing units in Chakan MIDC and Bhosari under Factories Act 1948 should provide factory licence and overtime register. IT companies in Hinjewadi SEZ units should confirm if they have separate PF establishment codes for SEZ and DTA operations.

Common Payroll Challenges in Pune

ChallengeImpactHow Patron Accounting Solves It
Labour Code Wage RestructuringCode on Wages mandates basic pay at 50%+ of CTC. Increases EPF/ESIC bases. Many Hinjewadi IT firms still on pre-2025 non-compliant structuresPatron restructures salary components to meet 50% basic requirement while optimising take-home pay
PTRC Filing ComplexityMulti-location employers need separate PTRC returns per city on mahagst.gov.in. FY 2025-26 due 15 March 2026PTRC returns filed for all Maharashtra locations. Deadline tracked and met without penalty
EPF Compliance for Growing StartupsCrossing 20-employee threshold triggers retrospective contributions + 12% interest + Section 14B damagesProactive EPF registration before threshold. Zero backdated liability risk
Overtime Errors in ManufacturingFactories Act 1948: overtime at 2x ordinary rate. Chakan/Bhosari units with multiple shifts prone to errorsAccurate overtime computation per Factories Act for all shift patterns
Form 16 Delays and TDS MismatchesDelayed Form 24Q or TDS computation errors create Form 26AS mismatches triggering IT scrutiny noticesForm 24Q filed quarterly on time. Form 16 by 15 June. Zero mismatches between Form 16 and Form 26AS

Payroll Service Fees in Pune

Fee ComponentAmount
Patron Accounting Professional Fees (Payroll Services)Starting from INR 2,999 (Exl GST and Govt. Charges)
Payroll Setup + Onboarding (one-time)Rs 4,999 - Rs 9,999
Monthly Payroll (up to 10 employees)Rs 1,499/month (all statutory compliances included)
Monthly Payroll (11-50 employees)Rs 3,999/month
Monthly Payroll (51-200 employees)Rs 7,999/month
TDS Filing (Form 24Q)Rs 999/quarter
Form 16 GenerationRs 99/employee (annual, by 15 June)
Full & Final SettlementRs 499/employee

All fees and charges listed are indicative only and do not constitute a binding offer. Final amounts may vary depending on the volume of work and the complexity involved.

Professional service charges for drafting, filing, and representation are separate from the statutory fees. The exact fee depends on the complexity of the case, disputed amount, and number of hearings required. Contact us for a detailed quote.

Get a free Payroll Services in Pune consultation - Call +91 945 945 6700 or WhatsApp us. No-obligation assessment.

Payroll Service Timeline in Pune

StageEstimated Timeline
Initial Assessment1 working day
Payroll Setup + Configuration2-3 working days
Data Migration (if switching)2-3 working days
First Payroll RunBy 1st of following month
First Compliance FilingBy 15th of following month
Total Setup3-5 working days

Note: EPF deposit by 15th - late payment triggers 12% interest + Section 14B damages (5-100% of arrears). ESIC by 15th. TDS by 7th. PTRC for FY 2025-26 by 15 March 2026. Code on Wages: 50% basic of CTC - non-compliant structures risk backdated recalculation. Every missed deadline compounds into larger penalties.

Key Benefits

Why Choose Patron for Payroll Services in Pune

Pune Office with EPFO/ESIC Experience

RTC Silver, Wagholi - within 30 minutes of Hinjewadi, Kharadi, Chakan MIDC. Walk-in for salary structure design, compliance reviews, and payroll audit support.

CA-Backed Processing

Every payroll run verified by CA team. Integrates with Tally/Zoho Books accounting, TDS returns, and statutory audit. Not just software-driven - audit-integrated.

All Compliance Included

EPF + ESIC + TDS + PT + LWF all in one monthly fee. No separate charges per compliance. Salary by 1st, EPF/ESIC by 15th, TDS by 7th, Form 16 by June 1st.

Track Record

10,000+ businesses served. 4.9 Google rating. 50,000+ documents filed. Zero late filing penalties guaranteed. 200+ employee payrolls handled monthly without errors.

Trusted by Employers Across Pune

10,000+ Businesses Served | 4.9 Google Rating | 50,000+ Docs Filed | 15+ Years

"Patron's payroll team handles 200+ employees without a single error month on month." - HR Head, IT Company, Gurugram

Trusted by Hyundai, Asian Paints, Bridgestone and businesses across India.

In-House Payroll vs Patron CA-Managed Payroll

FeatureIn-House PayrollPatron CA-Managed
Staff RequiredDedicated payroll executive (Rs 25,000-40,000/month)No additional hire needed
Compliance AccuracyDependent on individual's knowledgeCA-verified every month
EPF/ESIC FilingManual; risk of late filing penaltiesFiled by 15th without fail
TDS/Form 16Often delayed; mismatch riskForm 16 by 1 June; zero mismatches
Audit ReadinessYear-end scramble to compile recordsAudit-ready data maintained throughout year
Cost (50 employees)Rs 40,000+/month (salary + software + penalties)Rs 3,999/month (all-inclusive)

Legal and Compliance Framework for Payroll in Pune

Governing Acts:

  • EPF Act, 1952 - 12%+12% on basic+DA. 20+ employees. Section 14B damages (5-100%)
  • ESI Act, 1948 - 0.75%+3.25%. Salary up to Rs 21,000. 10+ employees in Maharashtra
  • Income Tax Act - Section 192 TDS on salary. Form 24Q quarterly. Form 16 by 15 June
  • Maharashtra PT Act 1975 - PTRC/PTEC mandatory. Male Rs 7,500/month. Max Rs 2,500/year
  • Code on Wages 2019 (Nov 2025) - Basic pay at least 50% of CTC
  • Payment of Gratuity Act 1972 - 5 years continuous service. Last drawn salary x 15/26 x years

Key Portals:

  • EPFO - epfindia.gov.in
  • ESIC - esic.gov.in
  • Maharashtra PT/LWF - mahagst.gov.in

FAQs - Payroll Services in Pune

Find answers to common questions about payroll services in Pune.

Quick Answers

Payroll outsource karna chahiye ya in-house rakhein? Agar 10+ employees hain aur dedicated HR/payroll person nahi hai, toh outsource cost-effective. EPF, ESIC, TDS, PT sab ka compliance automatic.

EPF ka paisa kab jama karna hota hai? Har mahine ki 15 tareekh tak. Late deposit pe Section 14B ke under 5% se 100% tak damages.

Maharashtra mein Professional Tax kitna lagta hai? Male: Rs 7,500/month se zyada salary pe. Max Rs 2,500/year. Female: Rs 25,000/month threshold.

Get Payroll Compliant in Pune Before the Next Cycle

EPF by 15th - late = 12% interest + 5-100% damages. ESIC by 15th. TDS by 7th. PTRC for FY 2025-26 by 15 March 2026. Code on Wages: 50% basic of CTC - non-compliant structures risk backdated recalculation. Every missed deadline compounds into larger penalties.

Start now - Call +91 945 945 6700 or WhatsApp us.

Get Payroll Services in Pune with Patron Accounting

Payroll services in Pune cover end-to-end salary processing, EPF/ESIC/TDS/PT statutory compliance, payslip generation, and Form 16 delivery for IT companies, manufacturers, startups, and professional services firms.

Patron Accounting's Pune office at RTC Silver, Wagholi delivers CA-managed payroll integrating with accounting, tax filing, and statutory audit. With 10,000+ businesses served and direct experience at Regional PF Commissioner and ESIC Regional Office Pune, your business meets every statutory deadline without penalty risk.

Book a Free Consultation - No Obligation.

Payroll Services Across India

Patron provides payroll services in 8 major cities.

Content Created: 13 March 2026  |  Last Updated: 13 March 2026  |  Next Review: 13 June 2026  |  Reviewed By: CA & CS Team, Patron Accounting LLP

This page is reviewed quarterly (Freshness Tier 1) to incorporate labour code changes, EPF/ESIC rate revisions, TDS computation updates, and Maharashtra PT deadline notifications. Content accuracy is verified by CA & CS Team, Patron Accounting LLP.

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