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GST Audit Service in Pune: Reconcile, Certify, and Stay Compliant

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Who Needs It: All GST-registered businesses in Pune with aggregate turnover exceeding Rs 5 crore must file GSTR-9C

What We Cover: GSTR-9C preparation, GSTR-9 vs books reconciliation, ITC reconciliation (2B vs books), DRC-03, S.65/S.66 defence

Due Date: 31 December following the relevant financial year

Late Fee: Rs 200/day (Rs 100 CGST + Rs 100 SGST), capped at 0.50% of turnover | Penalty Rs 25,000 for non-filing

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GST Audit Service in Pune - Overview

📌 TL;DR - GST Audit in Pune Services at a Glance

GST audit covers GSTR-9C reconciliation for businesses with turnover >Rs 5 crore, plus voluntary health checks and departmental audit defence. Since FY 2020-21, GSTR-9C is self-certified (CA certification no longer mandatory per Finance Act 2021). But professional CA assistance remains critical: GSTR-9C requires reconciliation of audited financials with GSTR-9 across 5 parts - turnover, tax paid, ITC claimed, additional liability, and unreconciled amounts. Discrepancies need DRC-03 payment. Due 31 December. Late fee Rs 200/day, capped at 0.50% of turnover.

Pune's diverse businesses create unique GST audit challenges. MIDC manufacturers (ITC on capital goods, job work). Hinjewadi IT companies (export/LUT, refund reconciliation). Camp wholesalers (multi-GSTIN, B2C). Koregaon Park professionals (RCM). Real estate developers (ITC reversal). Related: GST Audit across India and GST Returns in Pune.

Filed on gst.gov.in. GST Commissionerate Pune (CGST); Maharashtra GST (SGST). CBIC at cbic.gov.in. Related: GST Notice in Pune and Accounting Services.

Content is reviewed quarterly for accuracy.

Types of GST Audit

GSTR-9C (Self-Certified): Mandatory annual filing for turnover >Rs 5 crore. Reconciles audited financials with GSTR-9. 5-part reconciliation: turnover, tax, ITC, additional liability, unreconciled. Due 31 December.

Departmental Audit (S.65): Commissioner-initiated. Records examined. Complete within 3 months. Findings lead to S.73/74 demand. Special Audit (S.66): During investigation; external CA/CMA appointed; govt pays. Voluntary Health Check: For businesses approaching Rs 5 crore or wanting ITC/return cleanup. Related: ITR for Business in Pune and Pvt Ltd Compliance in Pune.

Key Terms for GST Audit in Pune:

  • GSTR-9C: Reconciliation statement for >Rs 5 crore. Self-certified since FY 2020-21. Due 31 December. Per-GSTIN filing.
  • S.65 Departmental: Commissioner audit. 15 working days notice. 3 months (+6). Discrepancies = S.73/74 demand.
  • S.66 Special: External CA/CMA during investigation. Govt cost. Report 90 days (+90).
  • DRC-03: Voluntary payment for additional liability found during reconciliation.
  • Aggregate Turnover: PAN-level. Taxable + exempt + export + inter-state. Rs 5 crore = GSTR-9C trigger for all GSTINs.
  • Rule 42/43: Proportional ITC reversal when exempt supplies exist.
9C GST Audit in Pune
GSTR-9C + DRC-03 Reconcile | Certify | File by 31 Dec

Who Needs GST Audit Service in Pune?

MIDC Manufacturers (Bhosari, Chakan): Turnover >Rs 5 Cr. Complex ITC on capital goods, job work (Rule 45), inter-state. Production vs invoice-basis reconciliation. Rule 42/43 reversals. Related: TDS Return Filing in Pune.

IT Companies (Hinjewadi, Kharadi): Export under LUT (zero-rated). Refund reconciliation. Forex differences. Multi-state GSTINs. Related: ITR for Companies in Pune.

Wholesalers + Real Estate (Camp, Baner, Wakad): High-volume B2B. Multiple GSTINs. Credit/debit notes. E-way bill. ITC reversal on unsold inventory. Related: Annual ROC Filing in Pune.

Professionals + Approaching Threshold: RCM compliance. SAC invoicing. Businesses at Rs 3-5 Cr should do voluntary health check before GSTR-9C becomes mandatory. Related: GST Returns for Restaurants in Pune.

GST Audit Services in Pune

ServiceWhat We Do
GSTR-9C Preparation + FilingEnd-to-end: audited financials, reconcile turnover (books vs GSTR-9), reconcile tax paid, reconcile ITC (books vs 2B vs returns), compute additional liability, DRC-03 payment, self-certify, file by 31 December. Per-GSTIN for multi-GSTIN businesses.
Turnover + ITC ReconciliationTurnover: match P&L with GSTR-9 Table 4/5. Explain: non-GST income, unbilled revenue, credit notes, timing. ITC: match books with 2B and GSTR-9 Tables 6-8. Identify reversals, supplier defaults, cross-year adjustments. Automated 2B-vs-books matching tools. Related: GST Returns in Pune.
Departmental Audit Representation (S.65)Provide records systematically, prepare reconciliation workpapers, respond to observations, negotiate findings. Post-audit demand notice response. Related: GST Notice in Pune.
Special Audit Coordination (S.66)Coordinate with appointed CA/CMA, provide records and explanations, represent taxpayer interests, response to special audit report.
Voluntary GST Health CheckFor below Rs 5 Cr or interim review: GSTR-1 vs 3B consistency, ITC vs 2B, RCM compliance, e-invoicing, HSN reporting, return filing accuracy. Pre-GSTR-9C readiness.
Our Process

GSTR-9C Filing Process in Pune

Our Pune CA team manages the complete GSTR-9C - from audited financials through reconciliation to certified filing.

Step 1

Obtain Audited Financial Statements

GSTR-9C starts with audited P&L, balance sheet and trial balance. Ensure statutory audit is complete and financials finalised. GSTR-9C Part II (turnover) and Part IV (ITC) must match audited figures. For multi-GSTIN businesses: PAN-level financials allocated to each GSTIN. Start in October after statutory audit completion.

Audited financials finalisedGSTIN-level allocation prepared
AuditedFinancialsP&L + BSStep 1
Financials Ready01
Step 2

Prepare GSTR-9 Annual Return

GSTR-9C is filed along with GSTR-9. Ensure GSTR-9 is complete: Table 4 (outward supplies), Tables 6-8 (ITC), Table 9 (tax paid), Tables 10-11 (amendments), Table 14 (differential tax). GSTR-9 must be filed before or simultaneously with GSTR-9C. Patron prepares both together for consistency.

GSTR-9 complete and verifiedAll tables reconciled
GSTR-9Annual ReturnPrepare
GSTR-9 Ready02
Step 3

Reconcile Turnover (Part II)

Compare gross turnover in audited P&L with GSTR-9 Table 4/5. Identify and document every difference: non-GST income (interest, dividends, rent from residential), unbilled revenue, advance billing, credit/debit notes, export under LUT (zero-rated), exempt supplies, timing differences between accrual-basis books and invoice-basis returns. Must explain 100% of variance.

Turnover variance 100% explainedAll legitimate differences documented
Books vsGSTR-9Part IITurnover Recon
Turnover Matched03
Step 4

Reconcile ITC (Part IV)

The most complex part. Compare total ITC in books with ITC in GSTR-2B and GSTR-9 Tables 6-8. Identify: ITC available but not claimed, ITC claimed but not in 2B (supplier default), reversals under Rule 37/37A/42/43, ITC on capital goods (phased), ITC on job work, cross-year adjustments. Patron uses automated 2B-vs-books matching tools for MIDC manufacturers with hundreds of suppliers.

ITC fully reconciledReversals computed and documented
Books vs 2Bvs ReturnsPart IVITC Recon
ITC Matched04
Step 5

Compute Additional Liability and File DRC-03

If reconciliation reveals additional tax (underreported turnover, excess ITC, rate differences), compute additional CGST/SGST/IGST and pay via DRC-03 on gst.gov.in before filing GSTR-9C. Part V of GSTR-9C captures these. Proactive DRC-03 payment before departmental notice reduces penalty risk.

Additional liability computedDRC-03 paid before filing
DRC-03Additional TaxPart VPay Liability
Liability Cleared05
Step 6

Self-Certify and File on GST Portal

Upload completed GSTR-9C on gst.gov.in with audited financial statements (PDF). Self-certify the reconciliation. File before 31 December. Save acknowledgement and ARN. For multi-GSTIN: file separate GSTR-9C for each GSTIN. Patron files and tracks for all Pune clients.

GSTR-9C self-certified and filedARN saved for all GSTINs
Filed by 31 Dec
Filed06

Documents Required for GST Audit in Pune

  • Audited Financial Statements: P&L, balance sheet, notes and auditor report for relevant FY.
  • Trial Balance: GSTIN-wise and HSN-wise for multi-GSTIN businesses.
  • GSTR-1 / GSTR-3B Annual Summaries: Monthly data for full year from portal.
  • GSTR-2B Summaries: Monthly April to March for ITC reconciliation.
  • Sales + Purchase Registers: Taxable, exempt, nil-rated, zero-rated, exports. HSN-wise.
  • ITC Ledger: Books vs returns with reversal details (Rule 37/37A/42/43).
  • Credit/Debit Notes: With cross-year adjustments.
  • DRC-03 Challans: Voluntary payments during the year.
  • E-Invoice Register: For e-invoicing applicable businesses.

Pune-specific tip: MIDC manufacturers: maintain separate job work register (Rule 45) and capital goods ITC schedule. Hinjewadi IT companies exporting under LUT: maintain refund reconciliation register (LUT supplies vs refund claimed vs received). Camp multi-GSTIN traders: prepare GSTIN-level trial balance allocation before starting GSTR-9C.

Common GSTR-9C Issues in Pune

ChallengeImpactHow Patron Accounting Solves It
GSTR-1 vs GSTR-3B Turnover MismatchCredit notes not in 3B, advances in 3B not in 1, amendments, table mapping errorsPatron prepares month-by-month GSTR-1 vs 3B comparison identifying and explaining every variance
ITC in Books vs GSTR-2BSupplier filed late, wrong GSTIN, no GSTR-1, Rule 37A reversal. MIDC manufacturers with 200+ suppliersPatron uses automated 2B-vs-books matching tools; flags supplier-level mismatches for resolution
Export Under LUT Zero-Rated ReconciliationHinjewadi IT: forex differences between books (RBI rate) and GST returns (invoice date rate)Patron prepares forex conversion variance analysis and reconciles with refund applications
Multi-GSTIN AllocationCamp wholesalers with 3+ GSTINs: PAN-level financials must be allocated per GSTINPatron prepares GSTIN-level trial balance allocation and files separate GSTR-9C for each

GST Audit Fees in Pune

Fee ComponentAmount
GSTR-9C (Single GSTIN, Rs 5-10 Cr)Patron Rs 15,000-30,000
GSTR-9C (Single GSTIN, Rs 10-50 Cr)Patron Rs 25,000-50,000
GSTR-9C (Single GSTIN, > Rs 50 Cr)Patron Rs 50,000-1,50,000
Multi-GSTIN (per additional GSTIN)Patron Rs 10,000-25,000
GSTR-9 + 9C Combined PackagePatron Rs 20,000-60,000
Voluntary GST Health CheckPatron Rs 8,000-20,000
Departmental Audit Representation (S.65)Patron Rs 25,000-1,00,000
Special Audit Coordination (S.66)Patron Rs 50,000-2,00,000

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 GST Audit in Pune consultation - Call +91 945 945 6700 or WhatsApp us. No-obligation assessment.

GST Audit Timeline

StageEstimated Timeline
Statutory audit completionBy September-October
GSTR-9 preparationOctober-November
GSTR-9C reconciliationNovember-December
DRC-03 payment (if additional liability)Before GSTR-9C filing
GSTR-9C self-certification and filingBy 31 December
Departmental audit (if notified)As per notice; typically 3-6 months

Best practice: Start GSTR-9C in October immediately after statutory audit. Waiting until December risks missing the 31 December deadline. Pune businesses with complex reconciliations (MIDC, multi-GSTIN) should start by September. Late fee: Rs 200/day capped at 0.50% of turnover. A Rs 10 Cr business faces max Rs 5,00,000 late fee. Patron manages from RTC Silver, Wagholi.

Key Benefits

Why Choose Patron for GST Audit in Pune?

Pune Industry Expertise

MIDC manufacturers (ITC, job work, inter-state), Hinjewadi IT (export/LUT, refund), Camp wholesalers (multi-GSTIN, high-volume B2B). Industry-tailored reconciliation workpapers.

Automated Reconciliation Tools

Automated 2B-vs-books matching, GSTR-1 vs 3B comparison, HSN-level variance analysis. Catches mismatches early. Clean filing with zero surprises.

GSTR-9 + 9C Combined

Prepare both together ensuring consistency between annual return and reconciliation. Issues identified and corrected during GSTR-9 itself.

Departmental Audit Experience

Represented Pune businesses in S.65 departmental audits by CGST/SGST Commissionerate. Know the process, focus areas and how to present records systematically.

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GSTR-9C Self-Certification vs Voluntary CA Audit

FactorSelf-Certification (Current)Voluntary CA Audit (Recommended)
MandatoryYes (turnover > Rs 5 crore)No (optional since FY 2020-21)
Who CertifiesTaxpayer (authorised signatory)Chartered Accountant
LiabilityOn taxpayer directlyShared with auditor (professional liability)
RigourDepends on internal capabilityIndependent professional examination; higher assurance
CostInternal effort onlyProfessional fees (offset by reduced risk)
Recommended ForStrong internal finance teamsNo dedicated GST team; complex operations; multi-GSTIN; export
Typical Pune CaseLarge IT company with internal tax teamMIDC manufacturer without internal GST expertise

Related Services

For Pune businesses needing related compliance:

Legal and Compliance Framework

Section 44 CGST Act: Annual return GSTR-9 by 31 December. Turnover >Rs 5 crore: self-certified GSTR-9C with audited financials.

Section 35(5) Omitted: Finance Act 2021 removed mandatory CA/CMA audit. Self-certification replaced it.

Rule 80(3): GSTR-9C for aggregate turnover >Rs 5 crore. Self-certified. Per-GSTIN filing.

GSTR-9C Structure: Part I (basic), Part II (turnover recon), Part III (tax paid recon), Part IV (ITC recon), Part V (additional liability/DRC-03).

Section 65: Departmental audit. 15 working days notice. 3 months (+6). Discrepancies = S.73/74.

Section 66: Special audit by CA/CMA. Commissioner orders during investigation. Govt cost. 90 days (+90).

Aggregate Turnover: PAN-level. If >Rs 5 crore, every GSTIN under PAN files GSTR-9C.

Late Fee: Rs 200/day, capped 0.50% of turnover. Penalty Rs 25,000 (S.125). gst.gov.in. cbic.gov.in.

FAQs - GST Audit Service in Pune

Find answers to the most common questions about GST audit and GSTR-9C in Pune.

Quick Answers

GST audit kya hota hai? GSTR-9C ek reconciliation statement hai jo Rs 5 crore se zyada turnover wale ko file karna hai - audited accounts ko GST returns se match karna. Ab CA mandatory nahi (Finance Act 2021) - self-certify. Lekin CA ki madad zaroori hai complexity ke liye.

Due date? 31 December. Late fee Rs 200/day, max 0.50% of turnover.

Rs 5 crore se kam? GSTR-9C nahi chahiye. Lekin voluntary health check karwana accha practice hai.

GSTR-9C Due 31 December - Start Reconciliation Now

The 31 December deadline is firm. MIDC manufacturers with 200+ suppliers, Hinjewadi IT companies with export/LUT and Camp multi-GSTIN traders need 30-60 days of focused work. Starting in November means rushing - rushed GSTR-9C filings contain errors triggering scrutiny. ITC errors can result in demands of lakhs. Late fee for Rs 10 Cr turnover: max Rs 5,00,000. Professional fee (Rs 15,000-60,000) is negligible vs risk.

Start your GSTR-9C now - Call +91 945 945 6700 or WhatsApp us. Free consultation.

GST Audit in Pune - Reconciled, Certified, Compliant

GST audit and GSTR-9C is a critical annual compliance for Pune businesses with turnover exceeding Rs 5 crore - from MIDC manufacturers reconciling complex ITC to Hinjewadi IT companies matching export/LUT transactions to Camp wholesalers allocating across multiple GSTINs.

Patron Accounting's Pune office at RTC Silver, Wagholi provides dedicated GST audit - GSTR-9 and GSTR-9C preparation, turnover and ITC reconciliation, DRC-03 payment, departmental audit representation (S.65) and special audit coordination (S.66).

With 15+ years experience, 10,000+ businesses served and a 4.9 Google rating, Patron serves businesses across Pune, Mumbai, Delhi and Gurugram.

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Content Created: 23 March 2026  |  Last Updated:  |  Next Review: 23 September 2026  |  Reviewed By: CA & CS Team, Patron Accounting LLP

This page is reviewed semi-annually to reflect GSTR-9C format changes, Finance Act amendments, CBIC notification updates, late fee changes and new table additions. Last review: March 2026. Next review: September 2026.

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