GST Audit Checklist

GST Audit Checklist 2026 – Complete GST Compliance Review Guide

A comprehensive GST Audit Checklist helps businesses review GST compliance, reconcile returns with books of account and identify potential tax exposures before or during a departmental GST audit.

Under the current GST framework, departmental audit may be conducted by GST authorities under Section 65 of the CGST Act. A Special Audit may also be directed under Section 66 in specified circumstances.

The earlier turnover-based requirement for specified taxpayers to obtain a GST audit from a Chartered Accountant or Cost Accountant has been discontinued. However, businesses may still face departmental audits, scrutiny, investigations, refund verification and other GST proceedings.

Businesses facing a departmental audit or requiring professional assistance with reconciliations, documentation and representation may refer to our GST Audit Services in India.

What is a GST Audit Checklist?

A GST audit checklist is a structured review of GST registrations, returns, books of account, input tax credit, tax payments, reconciliations and supporting records. It helps determine whether GST positions reported by a business are properly supported by accounting records and documentary evidence.

The checklist can be used while preparing for a departmental audit as well as for a voluntary internal GST compliance review.

Businesses may also refer to the official CBIC Assessment and Audit Rules for the prescribed GST audit procedure.

GST Audit Checklist at a Glance

GST Registration and Master Data

Verify GST registrations, legal name, trade name, principal place of business, additional places of business, authorised signatories and other registration particulars.

GST Returns and Turnover

Review GSTR-1, GSTR-3B, books of account and financial statements to identify differences in taxable, exempt and zero-rated turnover.

Input Tax Credit and GST Liability

Review GSTR-2B, purchase records, blocked credits, reversals, reverse charge liability, tax payments and electronic ledgers.

GST Registration and Records Review

GST Registration Details

Check whether:

• GST registration has been obtained wherever required;
• registrations are available in all applicable States or Union Territories;
• legal name and trade name are correct;
• principal and additional places of business are updated;
• authorised signatory details are current;
• business activities are correctly reflected; and
• necessary registration amendments have been filed.

For further guidance, refer to our GST Registration Procedure Guide.

Books of Account and GST Records

Businesses should maintain records capable of supporting the transactions reported in GST returns. Depending upon the nature of business, records may include sales registers, purchase registers, general ledgers, trial balances, stock records, fixed asset registers, invoices, debit notes, credit notes and supporting agreements.

Official requirements relating to records can be referred to under the CBIC Accounts and Records Rules.

Supporting GST Documents

Review whether tax invoices, bills of supply, delivery challans, payment vouchers, receipt vouchers, e-way bills, import documents and export records have been properly retained and can be linked with the accounting entries and GST returns.

GST Return and Turnover Reconciliation

GSTR-1 Review

Review outward supplies reported in GSTR-1 and verify taxable supplies, B2B invoices, B2C transactions, inter-State supplies, intra-State supplies, exports, debit notes, credit notes and amendments.

The values should be reconciled with the sales register and underlying invoices.

GSTR-3B Review

Verify taxable turnover, output tax liability, zero-rated supplies, exempt supplies, reverse charge liability, eligible input tax credit, ITC reversals and tax discharged through the electronic cash and credit ledgers.

GSTR-1 vs GSTR-3B Reconciliation

Compare outward supplies reported in GSTR-1 with the liability reported in GSTR-3B.

Differences may arise because of amendments, credit notes, debit notes, timing differences, omitted invoices, incorrect reporting periods or subsequent corrections. Material differences should be properly reconciled and documented.

GST Turnover vs Books and Financial Statements

Reconcile GST turnover with the sales ledger, trial balance and financial statements.

The reconciliation should consider taxable supplies, exempt supplies, exports, branch transfers, related-party supplies, advances, credit notes, debit notes, unbilled revenue and other income having possible GST implications.

Businesses may also read our GST Return Filing Process Guide.

Input Tax Credit Review

ITC Eligibility Review

Input tax credit should be examined with reference to the statutory conditions applicable to the relevant period.

Verify whether valid supporting documents are available, goods or services have been received, the credit relates to business purposes and other applicable conditions have been complied with.

GSTR-2B vs Purchase Register Reconciliation

Reconcile input tax credit recorded in the purchase register with GSTR-2B.

Identify invoices appearing in books but not in GSTR-2B, documents appearing in GSTR-2B but not in books, duplicate credits, incorrect GSTINs, credit notes, cancelled invoices, vendor reporting errors and other differences.

The GST Portal explains that GSTR-2B is an auto-drafted ITC statement and advises taxpayers to reconcile it with their own books and records. Refer to the official GST Portal GSTR-2B guidance.

Blocked ITC under Section 17(5)

Review expenditure that may be subject to restrictions under Section 17(5), depending upon the nature of the transaction and applicable exceptions.

Common review areas can include motor vehicles, food and beverages, club and membership expenses, works contract services, construction-related expenditure, personal consumption, gifts and free samples.

ITC Reversal Review

Check whether ITC reversals have been made wherever required. Review exempt supplies, non-business use, blocked credits, credit notes and other reversals prescribed under GST law.

Each reversal should be supported by a clear working and appropriate accounting treatment.

Reverse Charge, Invoice and Classification Review

Reverse Charge Mechanism Checklist

Review transactions potentially liable to GST under Reverse Charge Mechanism.

Check whether the applicable liability was identified, GST was discharged in the correct period, proper documentation was maintained and eligible ITC was subsequently claimed in accordance with applicable provisions.

Special attention may be required for import of services and other notified transactions.

Tax Invoice Checklist

Review whether tax invoices contain applicable prescribed particulars, including supplier details, GSTIN, invoice number, invoice date, recipient details, description, HSN or SAC, taxable value, GST rate and tax amount.

Debit Note and Credit Note Checklist

Review debit notes and credit notes issued or received during the relevant period. Verify linkage with the original transaction, GST impact, accounting entry, GST-return reporting and corresponding ITC impact where applicable.

HSN, SAC and GST Rate Checklist

Review classification of major goods and services and verify the applicable HSN, SAC and GST rate.

Special attention should be given to new products, new services, exemptions, concessional rates, composite supplies, mixed supplies and transactions where classification is uncertain.

Businesses may refer to our GST Tax Rate Guide for further information.

Place of Supply and Cross-Border Transactions

Place of Supply Checklist

Review the location of supplier, location of recipient and nature of the transaction to determine whether CGST/SGST or IGST has been applied correctly.

Particular attention may be required for inter-State services, immovable-property-related services, transportation, intermediary arrangements and transactions involving multiple States.

Export of Goods and Services Checklist

For export transactions, review export invoices, shipping bills, Letter of Undertaking where applicable, IGST payment where relevant, foreign inward remittances, place-of-supply conditions and reconciliation of export turnover with GST returns.

Businesses claiming GST refunds can refer to our GST Refund Services in India.

Import Transactions Checklist

Review bills of entry, customs documents, IGST paid on import of goods, import of services, reverse charge liability, related-party imports, foreign-currency payments and reconciliation with books and GST returns.

E-Way Bill, Job Work and Branch Transactions

E-Way Bill Checklist

Review whether e-way bills have been generated wherever applicable and whether key particulars correspond with the underlying invoice and actual movement of goods.

Check invoice number, date, taxable value, GSTIN, place of dispatch, place of delivery, transporter or vehicle particulars and validity.

For more information, refer to our E-Way Bill under GST Guide.

Job Work Checklist

Businesses sending goods for job work should review movement of goods, delivery challans, job-worker records, applicable GST reporting, ITC implications, return of goods and applicable statutory time limits for inputs and capital goods.

Related-Party Transaction Checklist

Review transactions between related parties and group companies, including management charges, reimbursements, intercompany services, common-cost allocations and transactions with foreign group entities.

Verify valuation, invoicing, GST rate and place-of-supply treatment.

Branch and Distinct-Person Transactions

Where an entity has GST registrations in more than one State, examine supplies between distinct persons.

Review cross-charges, inter-State branch transactions, common service allocations, invoicing, valuation, tax payment and corresponding ITC at the recipient registration.

GST Refund and Annual Compliance Review

GST Refund Checklist

For businesses claiming refunds, review eligibility, relevant period, refund computation, turnover, eligible ITC, supporting invoices, LUT, shipping bills, remittance evidence, electronic ledgers and reconciliation with GST returns.

You may also refer to our Guide to Documents for GST Refund Applications.

Annual Return and GSTR-9C Checklist

Where applicable, review GSTR-9 and GSTR-9C with the books of account and financial statements.

GSTR-9C under the current framework is a self-certified reconciliation statement where the applicable conditions are satisfied; it should not be confused with the earlier auditor-certified GST audit regime.

Annual Compliance Supporting Documents

Maintain appropriate workings for turnover, tax liability, input tax credit, previous-year adjustments and differences between GST returns and financial statements.

Financial Statements and Electronic Ledger Reconciliation

Financial Statement Reconciliation

Reconcile GST returns with final or audited financial statements.

Important areas include revenue from operations, other income, purchases, expenses, fixed assets, advances, receivables, payables, GST liability, input tax credit, exports, imports and branch transactions.

Electronic Ledger Checklist

Review the electronic liability register, electronic credit ledger and electronic cash ledger.

Verify whether tax payments, ITC utilisation, cash deposits, outstanding liabilities, adjustments and refunds reconcile with books of account.

GST Interest and Late Fee Checklist

Review whether interest or late fee became payable because of delayed tax payment, delayed return filing, incorrect tax treatment, ITC-related adjustments or other applicable defaults.

Any liability should be determined with reference to provisions applicable to the relevant tax period.

GST Departmental Audit Documents Checklist

Documents to Keep Ready after GST ADT-01

Depending upon the scope of the notice, commonly required documents may include:

• GST registration certificates;
• GSTR-1 and GSTR-3B;
• annual returns and GSTR-9C, where applicable;
• trial balance and general ledger;
• financial statements;
• sales and purchase registers;
• expense ledgers;
• fixed asset register;
• GSTR-2B reconciliations;
• ITC and RCM workings;
• tax invoices, debit notes and credit notes;
• e-way bills;
• export and import documents;
• refund records;
• contracts and agreements; and
• other documents specifically sought by the audit authorities.

Reconciliations to Prepare before Submission

Before submitting records, prepare key reconciliations such as GSTR-1 vs GSTR-3B, GST turnover vs books, ITC vs GSTR-2B, RCM workings and GST returns vs financial statements.

Explanations and Supporting Evidence

Material differences should be supported by transaction-level workings, contracts, invoices, accounting entries and legal explanations where required. A clear explanation prepared in advance can reduce unnecessary follow-up queries.

GST Departmental Audit under Section 65

GST ADT-01 Audit Notice

Where the department decides to conduct an audit under Section 65, the registered person is required to be informed through FORM GST ADT-01. The law provides that notice should be given at least 15 working days before the conduct of the audit.

GST Departmental Audit Process

The audit may involve verification of books, GST returns, turnover, exemptions, tax rates, input tax credit, refunds and other relevant matters.

A Section 65 audit is ordinarily required to be completed within three months from commencement of audit. The Commissioner may, for recorded reasons, extend the period by a further period not exceeding six months.

For comprehensive professional assistance, refer to our GST Audit Services in India.

GST ADT-02 Audit Findings

On conclusion of the audit, findings are communicated to the registered person through FORM GST ADT-02 in accordance with the applicable GST provisions and rules.

For further information about departmental functions, refer to our guide on Functions of GST Audit Commissionerate.

Special Audit under Section 66

When Can Special Audit Be Directed?

Under Section 66, an officer not below the prescribed rank may, with prior approval of the Commissioner and having regard to the nature and complexity of the case and the interest of revenue, direct a Special Audit where specified statutory conditions are present.

The audit is carried out by a Chartered Accountant or Cost Accountant nominated by the Commissioner.

FORM GST ADT-03 and ADT-04

The direction for Special Audit is issued through FORM GST ADT-03. On conclusion of the Special Audit, findings are communicated through FORM GST ADT-04.

The nominated auditor is generally required to submit the report within 90 days, subject to the statutory provision permitting a further extension of up to 90 days in appropriate circumstances.

Refer to the official CBIC Assessment and Audit Rules.

What Happens If GST Audit Finds a Discrepancy?

Responding to GST Audit Observations

Where discrepancies are identified during departmental audit, the taxpayer should understand the precise observation, reconcile the underlying data, verify the legal position, prepare supporting workings and submit a properly documented response.

Factual reconciliation differences should be distinguished from genuine tax disputes.

Further GST Proceedings

If the audit results in identification of tax short-payment, erroneous refund or input tax credit issues, further proceedings may arise under the applicable GST provisions.

Businesses requiring broader assistance with GST notices, assessments and litigation may refer to our GST & Indirect Tax Advisory Services in India.

How EzyBiz Assists with GST Audit Preparation

Pre-Audit GST Compliance Review

EzyBiz India Consulting LLP assists Indian and foreign-owned businesses with GST audit preparation and voluntary compliance reviews.

Our review may include GSTR-1 vs GSTR-3B reconciliation, turnover reconciliation, GSTR-2B and ITC review, blocked ITC, RCM, HSN/SAC classification, GST rates, place of supply, exports, imports, e-way bills and financial-statement reconciliation.

Departmental GST Audit Support

We assist businesses with review of GST ADT-01, preparation of documents and reconciliations, analysis of audit observations, preparation of factual and legal explanations and representation support during departmental proceedings.

For professional assistance, visit our GST Audit Services in India page.

Frequently Asked Questions on GST Audit Checklist

Is GST audit mandatory based on turnover?

No. The earlier turnover-based mandatory GST audit by a Chartered Accountant or Cost Accountant has been discontinued. Departmental audit under Section 65 and Special Audit under Section 66 continue under the GST framework.

Who conducts GST departmental audit?

A departmental audit under Section 65 may be undertaken by the Commissioner or an officer authorised by the Commissioner.

What is the most important GST audit reconciliation?

No single reconciliation applies to every business. Important reconciliations generally include GSTR-1 vs GSTR-3B, GST turnover vs books and financial statements, and ITC vs purchase records and GSTR-2B.

Should GSTR-2B be reconciled with the purchase register?

Yes. GSTR-2B should be reconciled with the taxpayer’s books and purchase records. However, reflection in GSTR-2B alone does not automatically establish ITC eligibility; the applicable statutory conditions should also be reviewed.

How much notice is given before a Section 65 GST audit?

The registered person is required to be informed at least 15 working days before the conduct of an audit under Section 65.

What is FORM GST ADT-02?

FORM GST ADT-02 is the prescribed form through which the findings of a departmental GST audit under Section 65 are communicated to the registered person.

Related GST and Tax Services

Businesses requiring professional GST and tax assistance may also explore:

• GST Audit Services in India – Departmental GST audit preparation, reconciliations, documentation and representation support.
• GST & Indirect Tax Advisory Services – GST advisory, assessments, notices, refunds, appeals and litigation support.
• GST Refund Services in India – Refund eligibility, computation, documentation, filing and departmental follow-up.
• GST Registration Procedure – Guidance relating to GST registration and registration compliance.
• Functions of GST Audit Commissionerate – Explanation of departmental GST audit functions and procedure.
• Who Can Do GST Audit in India? – Guidance on Section 65 departmental audit and Section 66 Special Audit.
• Can Statutory Auditor Do GST Audit? – Explanation of the current GST audit framework.
• E-Way Bill under GST – Guidance on e-way bill applicability and compliance.
• Tax and Regulatory Advisory Services in India – Integrated tax, GST and regulatory advisory support.

Reviewed By and Disclaimer

Reviewed By:
Anil Agrawal, Chartered Accountant
Founder, EzyBiz India Consulting LLP

Last Updated: September 2026

Disclaimer: This page provides general information and a broad GST audit checklist. The checklist is not exhaustive and the requirements applicable to a taxpayer depend upon its business, transactions, tax period and applicable GST provisions, rules, notifications and judicial interpretations. Professional advice should be obtained based on the specific facts and circumstances of each case.