GSTR-9 Annual Return
Reconciliation Checklist

Section 1: Pre-Filing Preparation

• ☐
  Gather all GSTR-1 filed during the year — April to March (monthly/quarterly)
• ☐
  Gather all GSTR-3B filed during the year — check if any amendments pending
• ☐
  Download auto-populated GSTR-9 from GSTN portal — compare Table-wise with actual data
• ☐
  Extract books of accounts summary — total turnover, taxable, exempt, nil-rated, non-GST
• ☐
  Reconcile turnover (Table 5) — books vs GSTR-1 vs GSTR-3B; document any differences
• ☐
  Check for amendments/credit notes — ensure reflected in GSTR-1 and books both
• ☐
  Verify advance receipts — advances received and adjusted during the year (Table 4)
• ☐
  Confirm cancelled/NIL-rated supplies — included under correct category

Section 2: Outward Supply Verification (Tables 4 & 5)

• ☐
  Table 4 — Taxable outward supplies: Verify B2B, B2C, export, SEZ with GSTR-1 aggregate
• ☐
  Table 5 — Exempt, nil-rated, non-GST supplies: Ensure all supply types classified correctly
• ☐
  Reconcile with GSTR-3B (Table 3.1) — total outward taxable should match within tolerance
• ☐
  Check exports (with/without payment) — LUT/bond status verified; IGST paid if applicable
• ☐
  Inward supplies attracting reverse charge — declared as outward in Table 4D
• ☐
  Taxable value match — GSTR-9 Table 4 vs GSTR-1 IGST/CGST/SGST columns

Section 3: ITC Reconciliation (Tables 6, 7 & 8)

• ☐
  Table 6A — ITC availed as per GSTR-3B: Sum all monthly GSTR-3B ITC (both auto and manual)
• ☐
  ITC as per GSTR-2B for the year: Download annual GSTR-2B summary from portal
• ☐
  Reconcile GSTR-2B vs books ITC: Identify mismatches > ₹10,000 — document reason
• ☐
  Table 6B — ITC on inputs: Capital goods ITC separated from inputs/input services
• ☐
  RCM ITC (Table 6C/6D): Verify RCM tax paid in 3B matches ITC claimed on RCM
• ☐
  ITC on imports (IGST): Bill of Entry data vs books; customs IGST credit taken correctly
• ☐
  Table 7 — ITC reversals: Rule 42 (mixed use), Rule 43 (capital goods), blocked credits (Sec 17(5))
• ☐
  Ineligible ITC (Table 7H): Motor vehicles, personal expenses, food, club — all reversed
• ☐
  Table 8 — ITC comparison: Verify auto-populated figures vs your working; explain excess or short
• ☐
  Net ITC (6 minus 7): Cross-check with electronic credit ledger balance

Section 4: Tax Payment Reconciliation (Tables 9 & 10)

• ☐
  Table 9 — Tax paid as declared in GSTR-3B: Sum all monthly tax paid (IGST/CGST/SGST/Cess)
• ☐
  Reconcile cash vs ITC payment split: Match Electronic Cash Ledger payment entries
• ☐
  Interest paid during the year: Include any interest paid for delayed filing/payment
• ☐
  Late fee paid: Capture all late fee paid in cash ledger during the FY
• ☐
  Table 10/11 — Previous year adjustments: Any amendments filed between April-September affecting previous FY
• ☐
  Difference in tax liability: If GSTR-9 reveals higher liability, pay via DRC-03 before filing

Section 5: HSN/SAC Summary (Tables 17 & 18)

• ☐
  Table 17 — HSN-wise outward supplies: Mandatory for taxpayers with turnover > ₹5 Cr (4-digit HSN); > ₹1.5 Cr (2-digit)
• ☐
  Table 18 — HSN-wise inward supplies: Mandatory for turnover > ₹5 Cr
• ☐
  Verify HSN codes: Match with product master; confirm correct digit level as per turnover slab
• ☐
  HSN taxable value & tax split: IGST/CGST/SGST correctly allocated per HSN line
• ☐
  Auto-populated HSN data: Review system data vs your working — correct any misclassifications

Section 6: Final Review Before Filing

• ☐
  GSTR-9C applicability: If turnover > ₹5 Cr, GSTR-9C (reconciliation statement) must be filed simultaneously
• ☐
  Nil return check: If no outward supply & no ITC, confirm nil GSTR-9 filing
• ☐
  Digital signature ready: DSC or EVC of authorised signatory working on GSTN portal
• ☐
  GSTR-9 preview: Download and review the JSON/PDF preview before submitting
• ☐
  Outstanding liabilities cleared: All DRC-03 payments done; no pending demands
• ☐
  File GSTR-9 before 31 December: Confirm ARN received and GSTR-9 status shows “Filed”

Quick Reference: Key Penalty Rates