GSTR 9C remains a useful audit ready document, even after the streamlining of recent years. This checklist is the one the firm uses internally for FY 2025-26 reconciliations, edited for client use.
Open the books and the GSTR data side by side
Pull turnover from the audited financials, GSTR 1 by month, GSTR 3B by month and GSTR 2B for ITC. Reconcile to the rupee. Differences typically arise from credit notes, advances, supplies under reverse charge and supplies to SEZ.
Verify ITC
Match ITC claimed in GSTR 3B with GSTR 2B and with the books. Identify ineligible credits taken, blocked credits under Section 17(5), credits required to be reversed under Rule 42 and 43 and credits time barred.
RCM, exports and SEZ supplies
Review reverse charge transactions, exports under LUT and supplies to SEZ. Confirm zero rated treatment, FIRC receipts where applicable, and shipping bill data.
Year end adjustments
Capture credit notes, debit notes, write offs, reclassifications and journal entries that affect turnover. Reconcile each adjustment to the relevant GSTR.
Documentation pack
Maintain a single binder that holds the reconciliation, supporting reports, sample testing memos and the final 9C with annexures. The binder is what the auditor signs off and is what the department reviews if scrutiny ever follows.