Eight Reconciliations That Prevent explained: this guide covers what it means, who it applies to, the step-by-step process, documents required, fees, due dates and penalties in India — so you can stay compliant with confidence and avoid costly mistakes.
Every system-generated intimation is a comparison of two datasets. Rule 88C compares GSTR-1 to GSTR-3B. Rule 88D compares GSTR-3B to GSTR-2B. Scrutiny compares everything to everything.
Run the same comparisons first, and there is nothing left to flag.
Eight reconciliations, in order: books to GSTR-1; GSTR-1 to GSTR-3B; GSTR-2B to the purchase register; GSTR-3B credit to GSTR-2B; e-way bills to outward supplies; RCM liability to inward supplies; Rule 42 and 43 reversal to exempt turnover; and the annual set — GSTR-9 to GSTR-3B to the financial statements.
1. Books to GSTR-1
Compares: the sales register to the outward supplies reported.
Prevents: understated turnover, missing invoices, and the GSTR-9 Table 4 variance.
When: before filing GSTR-1.
Fix window: GSTR-1A, before GSTR-3B. GSTR-1A →
2. GSTR-1 to GSTR-3B
Compares: liability declared to liability paid.
Prevents: DRC-01B under Rule 88C. Rule 88C and DRC-01B →
Standing differences to document: reverse charge outward supplies, credit notes, prior-period amendments, s.9(5) supplies.
3. GSTR-2B to the purchase register
Compares: what suppliers reported to what was recorded.
Prevents: unclaimed credit expiring under s.16(4), and credit claimed on invoices absent from 2B failing s.16(2)(aa).
When: after 2B generation on the 14th, before GSTR-3B.
Also catches: supplier non-filing, which is the Rule 37A exposure. Rule 37A →
4. GSTR-3B credit to GSTR-2B
Compares: credit availed to credit available.
Prevents: DRC-01C under Rule 88D. Rule 88D and DRC-01C →
Standing differences to document: imports on a bill of entry, self-assessed RCM credit, re-availment, ISD credit, prior-period credit.
5. E-way bills to outward supplies
Compares: movements documented to supplies reported.
Prevents: scrutiny under s.61 on undeclared supplies, and detention exposure under s.129.
Also catches: e-way bills generated and cancelled without a corresponding credit note, and movements on delivery challans that were never reconciled to a subsequent invoice.
6. RCM liability to inward supplies
Compares: reverse charge declared in GSTR-3B Table 3.1(d) to the notified categories in the purchase ledger.
Prevents: the single most common scrutiny finding — unpaid RCM on legal services, GTA, sponsorship, director's services, security services, and imports of services.
Also catches: RCM paid but credit not taken, and RCM credit taken where s.17(5) blocks it. Blocked credit and reverse charge →
7. Rule 42 and 43 reversal to exempt turnover
Compares: the reversal computed to the exempt turnover declared.
Prevents: a demand for short reversal with interest from 1 April of the succeeding year.
Watch: the s.17(3) additions — reverse charge outward supplies, securities at 1% of sale value, sale of land, and post-completion sale of building. Section 17(3) →
8. The annual set
Compares: GSTR-9 to the twelve GSTR-3Bs to the twelve GSTR-1s to the audited financial statements.
Prevents: GSTR-9C unreconciled differences, which are the starting point for most audits.
When: October and November, before filing GSTR-9 — because filing it closes the correction window. Section 37(3): the 30 November limit →
The calendar
| When | What |
|---|---|
| Through the month | IMS actions on incoming records |
| By the 11th | Books to GSTR-1; file GSTR-1 |
| 14th | GSTR-2B generated |
| 15th–18th | 2B to purchase register; RCM check; recompute 2B if needed |
| By the 20th | GSTR-1 to GSTR-3B; credit to 2B; Rule 42 monthly; file GSTR-3B |
| Quarterly | E-way bill to outward supply reconciliation |
| September–October | Full-year 2B reconciliation; identify unclaimed credit |
| By 20 November | Last corrections in the October GSTR-3B |
| Before 30 November | Rule 42 and 43 annual true-up |
| December | GSTR-9 and GSTR-9C, after everything above |
The two dates that matter most
The 20th of each month. Everything reconcilable for a period must be reconciled before GSTR-3B is filed, because filing closes the period's correction routes — GSTR-1A is gone, 2B cannot be recomputed, and the next chance is a subsequent period's amendment tables.
20 November. The October GSTR-3B is in practice the last return in which a financial year's corrections can be made, since the November return is filed in December — after the 30 November statutory limit.
Key takeaways
- Every automated intimation is a two-dataset comparison; run it first.
- GSTR-1 to GSTR-3B prevents DRC-01B; GSTR-3B credit to GSTR-2B prevents DRC-01C.
- Document the standing structural differences once, so each month's reply is a template.
- RCM to inward supplies is the most common scrutiny finding.
- The Rule 42 and 43 annual true-up carries interest from 1 April of the succeeding year.
- File GSTR-9 last, because filing it closes the correction window.
Read next
- Rule 88C and DRC-01B: GSTR-1 versus GSTR-3B
- Rule 88D and DRC-01C: ITC Availed versus Available
- Section 37(3): The 30 November Rectification Limit
- Section 61 Scrutiny: ASMT-10 and the Thirty-Day Reply
Disclaimer: Positions stated as on 5 September 2026, based on the CGST Act and Rules as amended to 31 March 2026 (ICAI Bare Law, 12th edition) and the ICAI Handbook on Returns and Payments under GST.