GST reconciliation is the process of matching your books with your GST returns and portal data: sales with GSTR-1, purchases with GSTR-2B, and both with the tax paid in GSTR-3B. Skip a month and the gaps pile up quietly, until twelve months of unexplained differences land on GSTR-9.
OneFinOps prepares each return from the ledger and hands you the differences with their causes, so the reconciliation exists before you file.
Key takeaways
- Monthly musts: purchase register vs GSTR-2B, and sales vs GSTR-1 vs GSTR-3B.
- Since the July 2025 tax period, GSTR-3B Table 3 comes from GSTR-1.
- ITC is limited to GSTR-2B under rule 36(4), shaped by your IMS actions.
Types of GST reconciliation
| Reconciliation | Compares | Frequency |
|---|---|---|
| Purchase register vs GSTR-2B | Your purchase invoices with supplier-reported ones | Monthly, before GSTR-3B |
| GSTR-2B vs GSTR-3B | ITC in 2B with ITC claimed in Table 4 | Monthly |
| Sales register vs GSTR-1 | Sales invoices, credit notes and advances | Monthly, before GSTR-1 |
| E-invoice and e-way bill vs GSTR-1 | IRNs and EWBs with GSTR-1 | Monthly |
| Books vs annual returns | Financial statements with GSTR-9 and GSTR-9C | Annually |
Rule 88D flags ITC in GSTR-3B that exceeds GSTR-2B by more than 20% and ₹25 lakh. Rule 88C flags GSTR-1 liability that exceeds GSTR-3B.
How to do GST reconciliation every month
- Close the books and post all invoices, credit notes and debit notes.
- Match the sales register with the IRN register and GSTR-1. File GSTR-1 by the 11th; fix errors in GSTR-1A before GSTR-3B.
- Act on IMS: accept correct supplier invoices, reject wrong ones, keep pending those awaiting delivery.
- After the 14th, match the purchase register to GSTR-2B: matched, value mismatch, in books only, in 2B only.
- Claim matched, eligible credit. Reverse blocked credit in Table 4B(1) and temporary items in Table 4B(2).
- File GSTR-3B by the 20th, then follow up with suppliers on anything missing.
GST reconciliation format in Excel
Put books and 2B data side by side on one key: supplier GSTIN plus invoice number, with spaces, slashes and leading zeros removed. Pull 2B columns with XLOOKUP on that key. Add taxable value and IGST, CGST, SGST from each side, a tax difference column, a status (matched, value mismatch, in books only, in 2B only) and the GSTR-3B table and owner. Allow a rounding tolerance, such as ₹10 per invoice.
Example. Mehta Trading Co has ₹8,40,000 of matched ITC, a Mumbai supplier who reported ₹16,200 against ₹18,000 in books, and a Surat supplier with ₹27,000 not reported. It claims ₹8,56,200 and chases ₹28,800. For the year-end version, see GSTR-9 and GSTR-9C.
How OneFinOps handles GST reconciliation
The Tax Agent prepares the return for each registration from the postings in the period, reconciles the purchase register to GSTR-2B line by line, and raises the follow-up against the vendor from the exception itself.
Two things always go to a person. A difference between return and ledger goes to the tax manager, with the cause stated. Every filing goes to the named preparer and reviewer before submission. The usual routine is exporting from books and rebuilding the match; here the return is assembled from the same ledger it is checked against, so filed and booked are one number.
