GST Audit Applicability & Limit in 2025: Who Needs to File & When?

During a recent discussion at our office about the latest GST Council updates, one important point that arose was the GST audit applicability and limits.

To clarify this key topic for businesses, we have compiled a comprehensive guide explaining who needs to file the GST audit report, applicable turnover thresholds, self-certification provisions, and critical deadlines.

This blog is meant to help Indian taxpayers navigate GST audit requirements confidently in 2025.

What is a GST Audit?

A GST audit involves reviewing a GST-registered taxpayer's records, returns, and documents to ensure the correctness of reported turnover, taxes paid, refund claims made, and input tax credit utilised.

It is one of the government's mechanisms to ensure compliance under the trust-based GST regime, where taxpayers self-assess their tax liability.

Types of GST Audits

• Turnover-based Audit: Initially required for businesses with a turnover above ₹2 crore (changed in 2021).
• General Audit: Conducted by GST officers on the commissioner's order, with prior notice.
• Special Audit: Ordered by GST authorities if discrepancies are suspected and conducted by a nominated CA or Cost Accountant.

Key Regulatory Update: Changes from FY 2020-21

• The government removed the mandatory GST audit by a CA or CMA for businesses with turnover over ₹2 crore from the financial year 2020–21 onwards.
• Taxpayers with turnover exceeding ₹5 crore now self-certify Form GSTR-9C instead of mandatory CA/CMA certification as per the Finance Act, 2021, and CBIC Notification No. 29/2021 dated 30th July 2021.
• This move aims to reduce compliance burden on medium-sized businesses while maintaining accountability through self-certification.

GST Audit Applicability & Threshold Limits in 2025

Aggregate Turnover	Requirement	Form to File
Up to ₹5 crore	No audit required; file annual returns only	GSTR-9
Above ₹5 crore	Self-certified GST audit report mandatory	GSTR-9C (self-certified)
Before FY 2020-21 (historical context)	CA/CMA audit mandatory for turnover above ₹2 crore	GSTR-9C (CA/CMA certified)

• Turnover thresholds are calculated on a PAN basis, i.e., total turnover of all GST registrations under the same PAN is considered.
• For taxpayers with aggregate turnover up to ₹5 crore, no audit certification is required; they must file GSTR-9 (annual return) without GSTR-9C.
• Taxpayers with turnover above ₹5 crore need to file a self-certified GSTR-9C along with the yearly return.
• For FYs before 2020-21, taxpayers exceeding ₹2 crore were required to get audited by a CA/CMA, but this requirement has been waived for subsequent years under various CBIC notifications.
• Compositions and e-commerce operators have their own forms (GSTR-9A and GSTR-9B).

What is Aggregate Turnover?

Aggregate turnover includes:

• Value of all taxable supplies (inter-state + intra-state)
• Exempt supplies
• Exports of goods and services
• Non-GST supplies
• Across all registrations under the same PAN.

GST Audit Process & Documentation

• Authorised Auditors:

Only a Chartered Accountant (CA) or Cost Accountant (CMA) can perform a GST audit under section 35(5) of the CGST Act. This applies only when an audit is mandatory for the taxpayer.

• Appointment Timing:

It’s best to appoint your GST auditor at the start of the financial year. This ensures ample time to prepare, avoid last-minute rush, and maintain compliance smoothly.

• Reconciliation of Records:

The core of the audit involves matching the turnover stated in your audited financial statements with the returns you have filed under GST. The auditor carefully verifies the claimed input tax credit (ITC) and checks for unpaid tax liabilities.

• Record Keeping:

Maintaining precise and detailed records throughout the year is crucial. This includes sales and purchase invoices, tax payment records, and updated books of accounts. Proper documentation makes the audit straightforward and reduces the chance of discrepancies.

• Final Audit Report (GSTR-9C):

The audit culminates in the preparation of Form GSTR-9C. This report highlights any issues found, reconciles tax liabilities, and provides a clear view of the taxpayer’s GST compliance status. This can be either self-certified or CA/CMA certified, depending on turnover and requirements.

Filing Deadlines

• Annual returns (GSTR-9) and audited reconciliation statements (GSTR-9C) are due by 31st December following the financial year.
• CBIC notifications may grant extensions.
• Failure to file within the stipulated deadlines may attract penalties.

Practical Insights & Compliance Tips

• Even if an audit is not mandatory due to turnover limits, maintain accurate records and file returns timely to avoid scrutiny.
• For taxpayers with turnover over ₹5 crore, ensure self-certification is done carefully to avoid errors.
• In case of multiple branches under one PAN, the combined turnover determines applicability; one auditor can be appointed for all branches for streamlined audit reporting.
• Consider engaging professionals for audit and filing assistance.

How Vyapar TaxOne Empowers GST Audit Compliance with Automation

• Smart Data Integration

Vyapar TaxOne effortlessly syncs data from popular accounting software like Tally, Vyapar, Excel, and GST portals, consolidating all critical information in one place for smooth audit processes.

• Maximised Input Tax Credit (ITC) Claims

Advanced AI-powered checks and reconciliations enable businesses to claim the maximum eligible ITC, reducing compliance gaps and audit risks.

• Simplified Document & Notice Management

Centralised management of invoices, notices, and audit-related documents keeps businesses organised and ready for any GST audit scrutiny.

• Time and Cost Efficiency

By automating repetitive accounting and compliance tasks, Vyapar TaxOne helps businesses save significant time and resources, allowing focus on core operations while staying GST-compliant.

Vyapar TaxOne is a robust GST automation solution that ensures compliance with audit applicability requirements and empowers businesses with precision, efficiency, and peace of mind during GST audits.

Staying well-informed and proactive ensures hassle-free GST audit compliance amid the dynamic regulatory environment.

FAQs

1. Who needs to file a GST audit report in 2025?

Businesses whose total annual turnover exceeds ₹5 crore are required to submit a self-certified GSTR-9C along with their annual return.

2. Is a CA/CMA mandatory for GST audit now?

No, compulsory CA/CMA audit for turnover over ₹2 crore was removed from FY 2020-21. Above ₹5 crore turnover, self-certification is allowed.

3. What is aggregate turnover for GST audit applicability?

It is the sum of taxable supplies, exempt supplies, and exports across all GST registrations under the same PAN.

4. What is the due date for GST audit filing?

The annual return and GSTR-9C must be filed by 31st December following the financial year, subject to extensions.

5. How can GST automation like Vyapar TaxOne help?

It automates reconciliations, generates audit reports, tracks deadlines, and integrates accounting data to simplify compliance.