Why This Reconciliation Is Non-Negotiable
The GST department runs automated reconciliation between GSTR-1 (outward supply details filed by you) and GSTR-3B (summary return with tax payment). If the output tax in GSTR-3B is lower than what you reported in GSTR-1, the department's system flags it as: "taxpayer collected tax from customers but did not deposit it."
This triggers a SCN (Show Cause Notice) under Section 73 (without fraud/suppression) or Section 74 (fraud/wilful suppression). Under Section 74, the penalty can be 100% of the tax shortfall.
What Exactly to Compare
| Item to Reconcile | GSTR-1 Table | GSTR-3B Table |
|---|---|---|
| B2B Taxable value + tax | Table 4A | Table 3.1(a) |
| B2C (large) taxable value + tax | Table 5 | Table 3.1(a) |
| B2C (small) taxable value | Table 7 | Table 3.1(a) |
| Zero-rated exports (with payment) | Table 6A | Table 3.1(b) |
| Zero-rated (without payment) | Table 6B | Table 3.1(b) |
| Nil-rated / Exempt | Table 8 | Table 3.1(c) |
| CDNs (Credit/Debit Notes) | Table 9A/9B | Table 3.1(a) |
| Advances received | Table 11A | Table 3.1(a) |
Top 5 Common Mismatches
1. Amendments not reflected in GSTR-3B
When you amend a B2B invoice in GSTR-1 using Table 9A/9B/9C, it changes the GSTR-1 totals. But GSTR-3B is not auto-updated — you must manually include the amendment difference in the current period's GSTR-3B.
2. Credit/Debit Notes treated differently
Credit notes reduce output tax in GSTR-1 Table 9. If you forget to reduce the corresponding amount in GSTR-3B Table 3.1, your 3B will show higher tax than GSTR-1 — creating a reverse mismatch that is harder to explain.
3. Advances received but not declared in GSTR-3B
If you received an advance in Month 1, tax on that advance must appear in GSTR-1 (as a receipt voucher) AND in GSTR-3B Table 3.1(a). Missing the GSTR-3B entry is one of the most common causes of mismatch.
4. Rounding differences across thousands of invoices
GSTR-1 is invoice-level (each row rounded). GSTR-3B is summary-level. Aggregated rounding across large invoice counts can create ₹1–₹500 differences. Document these with a reconciliation note to defend in case of query.
5. Wrong GSTIN of recipient in GSTR-1
Reporting a supply under an incorrect GSTIN means when you amend it, the original figure and amended figure both appear in GSTR-1 for different GSTINs. If GSTR-3B is not updated to match, it creates a mismatch.
How to Fix Mismatches
You overpaid. Adjust in the next GSTR-3B by reducing output tax under Table 3.1. Attach a reconciliation note in your records.
You underpaid. Pay the difference in the next GSTR-3B with 18% p.a. interest under Section 50(1), calculated from the original due date to the actual payment date.
Make a voluntary payment via DRC-03 (self-assessed tax) with applicable interest. Do not wait for a notice — voluntary disclosure reduces penalty risk significantly.
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