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A finance team files GSTR-1 and GSTR-3B straight from the accounting system and discovers mismatches only when a notice or a customer complaint arrives.
Four tie-outs in sequence: sales register to GSTR-1, GSTR-1 to GSTR-3B liability, purchase register to GSTR-2B, GSTR-3B to books. Each has a fixed slot in the month.
Monthly calendar with checks before the 11th, after the 14th and before the 20th; a one-page sheet per check with source A, source B, difference and reason.
Returns filed with every material difference explained in writing, and a monthly file that supports the annual return.
Before you file, tie out four things, in this order: the sales register with GSTR-1, GSTR-1 with the GSTR-3B liability, the purchase register with GSTR-2B, and the GSTR-3B totals with the GST ledgers in your books. Each check fits a fixed slot in the month, between the 1st and the 20th.
The checklist
| # | Check | Source A | Source B | Owner | When |
|---|---|---|---|---|---|
| 1 | Sales invoices complete | Sales register | Invoice series and e-invoice records | Billing | 1st to 5th |
| 2 | Sales match the return | Sales register | GSTR-1 draft | Accountant | Before the 11th |
| 3 | Credit notes and amendments | Credit note register | GSTR-1 credit note section | Accountant | Before the 11th |
| 4 | Supplier invoices reviewed | IMS on the portal | Purchase register | Accountant | Before the 14th |
| 5 | Credit matches the portal | Purchase register | GSTR-2B | Accountant | 14th to 17th |
| 6 | Liability matches GSTR-1 | GSTR-1 filed | GSTR-3B Table 3.1 | Accountant | Before the 20th |
| 7 | Reversals worked out | Reversal working | GSTR-3B Table 4(B) | Accountant | Before the 20th |
| 8 | Cash is available | Electronic cash ledger | GSTR-3B cash payable | Owner | By the 19th |
| 9 | Books tie to the return | GST ledgers in Tally or Zoho Books | GSTR-3B filed | Reviewer | After filing |
These dates are for monthly filers. QRMP filers follow a quarterly cycle, with GSTR-1 due by the 13th and GSTR-3B by the 22nd or 24th after the quarter.
What do you do first when the sales register and GSTR-1 disagree?
Check, in this order:
- Credit notes issued in the month but not in GSTR-1, or reported in GSTR-1 but not booked.
- Cancelled invoices still in one source.
- Invoice dates that fall in a different month in the two sources.
- B2B invoices reported as B2C, which means the customer’s GSTIN was not captured and the customer will not get credit.
- Tax rate errors, for example items still billed at a pre-revision rate after the GST rate changes of 22 September 2025.
Most gaps are explained by one or two of these.
How big a gap between the purchase register and GSTR-2B is just rounding?
A few rupees per invoice is rounding. Anything bigger has a cause, usually one of these: the supplier has not filed yet, the supplier is a quarterly filer, the invoice carries a wrong GSTIN, it was booked in a different month, or it is a blocked credit you should not claim anyway. List each gap by supplier and decide: claim, wait, or follow up.
For example, a purchase register showing ₹1,08,000 of ITC against a GSTR-2B of ₹1,07,996 is a ₹4 rounding gap; file. A register of ₹1,08,000 against a GSTR-2B of ₹90,000 is an ₹18,000 gap that needs supplier-by-supplier answers before the 20th. Remember that under Section 16(2)(aa) only the GSTR-2B figure can be claimed, and pending IMS invoices are deemed accepted when GSTR-2B is generated.
Worked example: a ₹59,000 gap
A Surat textile trader’s sales register for the month totals ₹6,40,000. The GSTR-1 draft shows ₹5,81,000. Gap: ₹6,40,000 minus ₹5,81,000 = ₹59,000.
Working through the list, the accountant finds a credit note of ₹59,000 issued on the 28th for returned goods. It was entered in GSTR-1 but was netted off in the register report under a different date filter. Once the register is re-run with the credit note included, both show ₹5,81,000. The whole gap is explained, and GSTR-1 is filed by the 11th with no change.
Without the check, the trader might have “corrected” GSTR-1 upward and overpaid tax on goods that came back.
How should a small team run this?
- Keep one sheet per check with four columns: Source A total, Source B total, difference, reason.
- Do not file until every difference has a reason.
- Save the sheets month by month. They are the backbone of the GSTR-9 annual return.
- Late filing costs a late fee under Section 47 and interest at 18% a year under Section 50, so do not let the checks push the return past the due date; file and correct next month if needed.
What to read next
For the detailed day-by-day version, read the GSTR-1 and GSTR-3B runbook for days 16 to 20 and the GSTR-2B ITC runbook for days 11 to 15. If you are new to the idea, start with what GST reconciliation means in simple words.
GST outward reconciliation (GSTR-1 and GSTR-3B) leads the TransactIG GST roadmap; inward matching (GSTR-2B, ITC, IMS) is on the roadmap. See the GST reconciliation page.