The Ultimate Guide to GST Reconciliation in TallyPrime (With the GST Portal)

Last month, I sat with a CA in Vijayawada whose client’s GSTR-3B showed more Input Tax Credit than the GST portal was willing to accept. The filing didn’t save. No warning, no notice — just a blank refusal.

That’s what GST reconciliation in TallyPrime is really about now. It’s not a nice-to-have anymore. Since April 2026, the portal blocks your GSTR-3B outright if your claimed ITC crosses your GSTR-2B. There’s no DRC-01C grace period to fall back on.

In this guide, I’ll walk you through the exact reconciliation routine I use with clients — matching your books to the GST portal, month by month, before the portal catches the gap for you.

Why Reconciliation Matters More in 2026

For years, mismatched ITC meant a warning. Under CBIC Notification 38/2023 (Rule 88D), GSTN would send a Form DRC-01C notice, and you’d get seven days to explain or pay the difference.

That safety net is gone. From April 2026, the portal enforces what’s often called a Zero Mismatch Policy. If the ITC in your GSTR-3B Table 4A exceeds what’s sitting in your GSTR-2B, the return simply won’t submit.

There’s a second clock running too. Under Section 16(4) of the CGST Act, you can only claim ITC on an invoice up to 30 November of the following financial year, or your annual return date — whichever comes first. Miss that window, and the credit is gone for good. No appeal fixes it.

Put both together, and reconciliation stops being a compliance checkbox. It’s the only thing standing between you and either a blocked filing or a permanently lost credit.

The Two Sides of GST Reconciliation

I tell every client the same thing: reconciliation isn’t one task. It’s two, running in opposite directions.

Sales-Side: What You Report vs What You Owe

This is your GSTR-1 against your books and your e-invoice register. If an invoice has an IRN but never made it into GSTR-1, or the numbers drift between the two, your buyer’s ITC is at risk — not just yours.

Purchase-Side: What You Claim vs What’s Available

This is your purchase register against GSTR-2B and the Invoice Management System (IMS). This side decides how much ITC you’re actually allowed to claim in GSTR-3B — regardless of what your books say you’re owed.

Most businesses only watch one side. The ones who avoid trouble watch both, every month.

Step-by-Step: Reconciling GSTR-2B in TallyPrime

GSTR-2B is a static ITC statement. The portal generates it on the 14th of every month and it doesn’t change after that — unlike GSTR-2A, which keeps updating as suppliers file late.

1. Download GSTR-2B from the GST portal for the return period, in JSON format.
2. Open TallyPrime and go to Gateway of Tally > Display More Reports > Statutory Reports > GST Reports > GSTR-2B Reconciliation.
3. Import the JSON file using Alt+I. TallyPrime reads the portal data straight into the report.
4. Review the three buckets TallyPrime creates: fully matched, potential matches (where GSTIN, document number, or amount differs slightly), and unmatched entries.
5. Resolve potential matches first. These are usually typos — a missing leading zero in an invoice number, or a rounding difference of a few rupees.
6. Chase unmatched entries. An invoice in your books with nothing in GSTR-2B means your supplier hasn’t filed, or you’re still Pending in IMS.

If you have more than one GSTIN, TallyPrime’s Connected GST feature lets you download and reconcile several registrations together in one pass, instead of switching companies each time.

Step-by-Step: Reconciling GSTR-1 and GSTR-3B

This is the sales side of the check, and CAs in Andhra Pradesh often skip it, focused only on ITC. It matters just as much — a mismatch here is what triggers your buyer’s DRC-01C, not yours.

1. Generate GSTR-1 from TallyPrime under Statutory Reports, and compare table totals against your sales register for the period.
2. Cross-check with your e-invoice register. Every B2B invoice above the e-invoicing threshold needs a matching IRN, dated within 30 days of the invoice date if your turnover is ₹10 crore or above.
3. Download the filed GSTR-3B and compare its summary values against GSTR-1 for the same period. A gap usually means an invoice was recorded in the wrong month.
4. Use TallyPrime’s one-click reconciliation to pull GSTR-1, GSTR-2B, and GSTR-3B together for the period and see all three side by side.

If you’re chasing a specific error message rather than doing a routine check, our guide on GSTR-1 and e-invoice errors in TallyPrime covers the five most common ones in detail.

Where IMS Fits Into the Picture

The Invoice Management System changed how GSTR-2B gets built. It’s been live on the GST portal since October 2024, and became mandatory for every GST-registered taxpayer from 1 April 2026. GSTN’s official IMS advisory covers the rollout in full.

Here’s the part people miss: an invoice your supplier files doesn’t automatically become your ITC anymore. It sits in IMS first, waiting for you to Accept, Reject, or leave it Pending.

• Accept — the invoice flows into your GSTR-2B as eligible ITC.
• Reject — it’s excluded, useful for invoices that aren’t yours or are duplicated.
• Pending — you’re holding it back for review, but it must be actioned before you file GSTR-3B.
• No action — treated as deemed accepted once your GSTR-3B deadline arrives.

TallyPrime’s connected IMS feature lets you pull your IMS queue, take these actions, and reconcile against your purchase register without switching to the browser. This is one more reason to keep your TallyPrime connected services active — if your TSS subscription lapses, this connected reconciliation stops working even though regular billing continues.

A Monthly Reconciliation Routine That Works

Here’s the routine I recommend to CA offices managing several GSTINs. It’s simple enough to run every month without eating a full day.

1. Week 1: Clear your IMS queue as invoices arrive. Don’t let it pile up till month-end.
2. Around the 11th: Confirm your suppliers have filed GSTR-1 or IFF. A missing filer means a missing GSTR-2B entry, whatever you do in IMS.
3. On the 14th: Import the fresh GSTR-2B into TallyPrime and run the reconciliation report the same day.
4. Before the 20th: Compare final ITC against your GSTR-3B draft. Resolve any gap before you file — not after.
5. Quarterly: Run a full-year ITC check against your GSTR-2B totals, so nothing quietly crosses the Section 16(4) deadline unnoticed.

GSTR-2A vs GSTR-2B vs IMS, Compared

If you want the government’s own explanation of how GSTR-2B is built, GSTN’s official GSTR-2B FAQ page is the primary source. Here’s how the three statements differ in practice:

For a broader look at how clean TallyPrime data supports return review and client sign-off, see our guide on TallyPrime for CAs, from bookkeeping to strategic growth.

Frequently Asked Questions

AtTally Sofper: Local Help With GST Reconciliation in TallyPrime

We’re AtTally Sofper Pvt. Ltd., an authorized Tally partner with offices in Visakhapatnam (Vizag) and Vijayawada.

For GST reconciliation, we help with:

• Setting up GSTR-2B and IMS reconciliation correctly inside TallyPrime, so your monthly routine actually works
• Fixing recurring GSTR-1 vs GSTR-3B mismatches for CA offices managing multiple client GSTINs
• Configuring e-invoicing and the 30-day reporting window for growing businesses
• TSS renewal, so connected reconciliation and IMS access never quietly stop mid-filing

We offer online and remote support, so most reconciliation fixes don’t need an office visit. If your GST filings keep hitting the same mismatch, reach out to our team. We’ll check your TallyPrime setup and sort it before your next deadline.