GST Audit Services — compliance under the data-driven tax regime.
GST annual return (GSTR-9), self-certified reconciliation (GSTR-9C), ITC audit and reconciliation, e-invoicing compliance, and full representation support for Section 65 departmental audits and Section 66 special audits under the CGST Act.
GST has become one of the most data-rich tax regimes in the world. Every invoice reported in GSTR-1 sits in your customer's GSTR-2B. Every e-invoice carries an IRN that the department can trace. Every ITC claim is matched against your supplier's filing in near real-time. The compliance footprint that used to take years to surface now does so in weeks — and departmental scrutiny, audits under Section 65, and demand notices have followed at the same pace.
The shift from CA-certified GST audit to self-certified GSTR-9C did not reduce the audit work — it transferred ownership of getting it right back to the taxpayer. ITC reversals under Rule 42 and 43. RCM payments that should have been made and were not. Blocked credits under Section 17(5). E-invoicing gaps. Classification errors between similar HSN codes. Each is a discrepancy waiting for the department's analytics to flag.
Our GST audit team handles the full spectrum — voluntary GST health checks before the annual return, GSTR-9 and GSTR-9C preparation and review, ITC audits across the year, e-invoicing compliance reviews, and end-to-end representation in Section 65 departmental audits and Section 66 special audits. The objective is straightforward: catch and correct issues before the department raises a demand, and represent the taxpayer effectively when it does.
GST Audit Services We Offer
GST Health Check / Diagnostic
Voluntary pre-audit review covering outward supplies, ITC, RCM, e-invoicing, and reconciliation — leakage and exposure quantified.
GSTR-9 Annual Return
Preparation, review, and filing of GSTR-9 — consolidating outward, inward, ITC, and tax data for the financial year.
GSTR-9C Reconciliation
Self-certified reconciliation statement linking audited financials with GSTR-9 — turnover, taxable value, ITC, and tax paid reconciled.
ITC Audit & Reconciliation
Review of ITC eligibility under Section 16, GSTR-2B matching, Rule 42/43 reversals, and blocked credits under Section 17(5).
Section 65 Department Audit
End-to-end support during departmental audit — documentation, written submissions, representation, and post-audit closure.
Section 66 Special Audit
Support during special audit nominated by the Commissioner — records compilation, liaison, and protective representations.
E-Invoicing & E-Way Bill Audit
Review of IRN generation, QR code compliance, credit/debit note e-invoicing, and e-way bill records under applicable thresholds.
HSN / SAC Classification Review
Validation of HSN and SAC codes, rate applicability, exemption claims, and place of supply for goods and services.
Our GST Audit Process
Scoping & Data Collection
Engagement scope, financial year coverage, identification of registrations, and data extraction from GSTN portal and ERP.
Books vs Returns Reconciliation
Reconciliation between books, GSTR-1, GSTR-3B, and GSTR-2B — identifying mismatches in turnover, tax, and ITC.
ITC & Reversal Review
Verification of ITC eligibility, Rule 42/43 reversals, RCM compliance, Section 17(5) blocked credits, and supplier non-compliance impact.
Compliance & Filing
GSTR-9 and GSTR-9C preparation, internal review, sign-off, and filing on the GST portal within statutory due date.
Department Audit Support
If selected for Section 65 or 66 audit — documentation, representation, and closure with minimal demand exposure.
Why GST Audit Matters
Frequently Asked Questions
The mandatory CA-certified GST audit under Section 35(5) of the CGST Act was removed by the Finance Act, 2021 — replaced by a self-certified reconciliation statement in Form GSTR-9C. The annual return in Form GSTR-9 continues to be mandatory for taxpayers with aggregate turnover exceeding the prescribed threshold (currently ₹2 crore), and GSTR-9C is required for taxpayers with turnover exceeding ₹5 crore. Many businesses still engage a CA to prepare and review these returns even though external certification is not legally required.
GSTR-9 is the annual return under GST, consolidating outward supplies, inward supplies, ITC claimed, ITC reversed, tax paid, and adjustments for the financial year. It is mandatory for every registered taxpayer with aggregate turnover exceeding ₹2 crore (or the threshold notified for the relevant year). Composition taxpayers file the simpler Form GSTR-9A, and e-commerce operators file Form GSTR-9B.
GSTR-9C is the reconciliation statement comparing the figures reported in the audited financial statements with those reported in GSTR-9. Following the Finance Act 2021 amendments, GSTR-9C is now self-certified by the taxpayer rather than certified by a Chartered Accountant. It is mandatory for taxpayers whose aggregate turnover exceeds ₹5 crore in the relevant financial year, and it must be filed along with the GSTR-9 by the due date.
Section 65 of the CGST Act empowers the GST Commissioner or an authorised officer to conduct an audit of any registered person. The audit must be completed within three months of commencement (extendable by six months), and the taxpayer must provide all records, facilities, and information needed. The audit can result in demand notices under Section 73 or 74. Our role in a Section 65 audit is preparation, representation, and managing the documentation flow with the department.
Section 66 allows the proper officer to direct a special audit by a Chartered Accountant or Cost Accountant nominated by the Commissioner, where the officer is of the opinion that the value declared is incorrect or ITC claimed is not within the normal limits. The special auditor reports within 90 days (extendable by 90 more). Findings can lead to demand notices and proceedings. Our involvement covers liaising with the special auditor, providing records, and supporting the taxpayer's representations.
An ITC audit is a review of input tax credit claimed by the business — verifying that each credit is eligible under Section 16, that the supplier has uploaded the relevant invoices in GSTR-1 (reflected in GSTR-2B), that ITC reversals are correctly computed under Rules 42 and 43, that blocked credits under Section 17(5) are not claimed, and that ITC on supplies received from cancelled or non-compliant vendors has been reversed. ITC audit findings often lead to recovery action by the department, so the review is best done internally first.
Even without statutory certification, voluntary GST audit makes sense because departmental audits under Section 65, GST scrutiny, and demand notices have become more frequent and data-driven. A pre-emptive review surfaces ITC reversals not made, RCM not paid, classification errors, e-invoicing gaps, and reconciliation issues — all areas where the department's analytical tools can flag mismatches. Catching these before the department does saves penalty and interest.
E-invoicing has been progressively extended to taxpayers with turnover above prescribed thresholds. An e-invoicing audit verifies that every invoice requiring an IRN (Invoice Reference Number) has been generated through the IRP, that QR codes are on invoices, that B2C QR provisions are followed where applicable, that credit notes and debit notes are also being e-invoiced, and that the e-invoicing data flows correctly into GSTR-1. Non-compliance attracts heavy penalties under Section 122.
Get a Defensible GST Position
Talk to our team about a GST health check, GSTR-9 / 9C preparation, ITC audit, or representation in a Section 65 / 66 departmental audit — surfaced and fixed before the demand notice arrives.
Talk to a GST Auditor or call +91 9819 000 511