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GST Audit and Annual Return – GSTR-9 & 9C Filing Guide (2025)

πŸ”Ή Introduction

Every registered taxpayer under GST must file annual returns summarizing yearly transactions. For certain taxpayers, a reconciliation statement (GSTR-9C) is also required to reconcile GST returns with audited financial statements. The GST audit framework ensures transparency, accuracy, and compliance in reporting turnover, tax liability, and ITC.

(Reference: Sec. 35(5) & 44 of CGST Act, Rule 80 of CGST Rules, CBIC notifications up to FY 2024-25)


πŸ”Ή Legal Framework & Applicability (As on FY 2024-25)

βœ… GSTR-9 – Annual Return

  • Mandatory for all registered persons (except composition dealers, ISDs, TDS/TCS deductors, and NRTPs).

  • Turnover limit for mandatory filing: Exceeding β‚Ή2 crore (though optional for those below β‚Ή2 crore as per latest CBIC relaxation).

βœ… GSTR-9C – Reconciliation Statement

  • Applicable if aggregate turnover exceeds β‚Ή5 crore during the financial year.

  • Taxpayers must self-certify GSTR-9C (audit by CA/CMA no longer mandatory as per amendments from FY 2021-22 onwards).


πŸ”Ή Key Differences – GSTR-9 vs GSTR-9C

Particulars GSTR-9 GSTR-9C
Purpose Consolidated annual return of GST data Reconciliation between books & returns
Applicability All regular taxpayers Turnover > β‚Ή5 crore
Certification Self-filed Self-certified (audit by CA/CMA removed)
Data Source GSTR-1, 3B, GSTR-2B Audited financial statements
Filing Type Compulsory Conditional

πŸ”Ή Step-by-Step Guide to File GSTR-9

πŸ“Œ Step 1: Log in to GST Portal

Visit www.gst.gov.in β†’ Returns β†’ Annual Return β†’ GSTR-9.

πŸ“Œ Step 2: Choose Financial Year

Select FY 2024-25.

πŸ“Œ Step 3: Auto-Populated Data

  • System auto-fills data from GSTR-1 & GSTR-3B.

  • Verify details (sales, tax liability, ITC, outward/inward supplies).

πŸ“Œ Step 4: Add/Edit Data

Make necessary corrections in:

  • Table 4: Outward supplies (taxable & exempt).

  • Table 6: ITC availed during year.

  • Table 8: ITC as per GSTR-2A/2B.

  • Table 9: Tax paid as per returns.

πŸ“Œ Step 5: Validate Data

Ensure totals of taxable value & tax match with books of accounts.

πŸ“Œ Step 6: Preview & File

Use DSC/EVC for submission. Download filed copy & acknowledgment.


πŸ”Ή Step-by-Step Guide to File GSTR-9C

πŸ“Œ Step 1: Access GSTR-9C on GST Portal

Navigate to Services β†’ Returns β†’ Annual Return β†’ GSTR-9C.

πŸ“Œ Step 2: Auto-Filled Data

System pulls data from GSTR-9 & financial statements.

πŸ“Œ Step 3: Sections to Fill

  • Part A – Reconciliation Statement:

    • Turnover, tax liability, rate-wise tax details.

    • Adjustments for unbilled revenue, advances, and credit/debit notes.

  • Part B – Certification:

    • Self-certification (by taxpayer).

πŸ“Œ Step 4: Validate & Submit

Use digital signature to file. Generate acknowledgment (ARN).


πŸ”Ή Due Dates, Late Fees & Penalties

  • Due Date: 31st December following the end of the financial year (FY 2024-25 β†’ 31st December 2025).

  • Late Fees (Sec. 47):

    • β‚Ή200 per day (β‚Ή100 CGST + β‚Ή100 SGST).

    • Maximum = 0.25% of turnover.

  • Penalty for Mismatch/Non-Filing: As per Sec. 125 & 74A for incorrect returns.


πŸ”Ή Documents Required

  • Audited financial statements (Balance Sheet, P&L).

  • GSTR-1, 3B, 2A/2B summary.

  • ITC register.

  • Reconciliation statements for turnover & tax paid.


πŸ”Ή Practical Examples

Example 1: Trader (Turnover β‚Ή3 crore)
Filing GSTR-9 mandatory; GSTR-9C not required.

Example 2: Manufacturer (Turnover β‚Ή6 crore)
Must file both GSTR-9 & GSTR-9C (self-certified).

Example 3: IT Service Provider (Turnover β‚Ή1.5 crore)
GSTR-9 optional (as per CBIC relaxation for <β‚Ή2 crore).


πŸ”Ή Common Errors in GSTR-9/9C Filing

  • Mismatch between GSTR-3B & GSTR-1 data.

  • Incorrect ITC carried forward.

  • Omission of credit notes/debit notes.

  • Reversal errors under Rule 42/43.

  • Late filing due to reconciliation delays.


πŸ”Ή Best Practices

  • βœ… Reconcile returns monthly & quarterly.

  • βœ… Conduct internal audit before year-end.

  • βœ… Verify ITC via GSTR-2B regularly.

  • βœ… File returns before due date to avoid late fee.

  • βœ… Maintain digital backup of all filings.


πŸ”Ή FAQs

Q1. Is audit by CA mandatory under GST?
➑️ No, self-certification is sufficient for GSTR-9C since FY 2021-22.

Q2. Can nil return filers skip GSTR-9?
➑️ Yes, if turnover < β‚Ή2 crore, filing optional.

Q3. What if turnover is β‚Ή5 crore exactly?
➑️ GSTR-9C required if turnover exceeds β‚Ή5 crore (i.e., > β‚Ή5,00,00,000).

Q4. Can GSTR-9/9C be revised?
➑️ No, once filed cannot be revised.

Q5. What if annual return not filed?
➑️ Heavy late fee & potential notice under Sec. 46 & 74A.


πŸ”Ή Conclusion

GSTR-9 & GSTR-9C provide a consolidated view of a taxpayer’s compliance during the year. Proper reconciliation with books ensures accuracy, avoids scrutiny, and maintains compliance credibility.

πŸ“Œ Need professional help in GSTR-9, 9C filing, or GST audit reconciliation?
Contact Tech-Tax Solutions – Quality, Trust & Expertise in Ghaziabad, Noida & Delhi.

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