🎁 Now live: Get 1 Month of Growth Tier Free when you sign up

India GST

GST reconciliation that protects your input tax credit

Last reviewed·ReconPe Editorial

Match your GSTR-2B against your purchase register and see the input tax credit you’re about to lose — invoices a supplier hasn’t filed — alongside the credit you haven’t claimed yet. Then match GSTR-1 to your sales and tie out GSTR-3B for a pre-file confirmation. One monthly close, in minutes.

Why GSTR-2B reconciliation eats month-ends

GSTR-2B is the gate for your input tax credit

Under Rule 36(4) and Section 16(2)(aa), you can only claim ITC on invoices that actually appear in your GSTR-2B. An invoice booked in your purchases but missing from 2B is credit you cannot take — until the supplier files.

A supplier who files late or wrong costs you cash

When a vendor misses their GSTR-1, your credit for that invoice is blocked for the month. Spread across dozens of suppliers, that is real working capital sitting frozen — and most teams find it only at quarter-end.

Invoice numbers and rounding never match cleanly

Your books write "INV/2026/0042"; the portal carries "INV-2026-42". Tax differs by a rupee from rounding. A VLOOKUP misses both, so genuine matches surface as mismatches and real gaps hide in the noise.

IMS and 3B locking changed the monthly routine

Since the Invoice Management System (Oct 2024), invoices flow through Accept / Reject / Pending before they land in 2B — and GSTR-3B is now hard-locked. The reconciliation has to be right before you file, not after.

GSTR-2A vs GSTR-2B: which one do you reconcile?

Short answer: GSTR-2B. It is the frozen, legally-operative statement your ITC claim is judged against — 2A is a moving reference.

GSTR-2AGSTR-2B
When it's generatedContinuously — updates as suppliers file and amendOnce a month, on the 14th, then frozen
Changes after generationYes — a moving targetNo — a fixed snapshot
What it's forTrend and audit referenceThe legal basis for your ITC claim (Rule 36(4) / Sec 16(2)(aa))
ITC eligibility markedNoYes — eligible/ineligible flags plus IMS Accept / Reject / Pending status
Which one to reconcileNot this oneThis one — 2B decides what you can claim

The rulebook that makes this non-optional: IMS, a locked 3B, and Rule 88D

Three changes turned GST reconciliation from good hygiene into a filing prerequisite. The Invoice Management System (since Oct 2024) routes every supplier invoice through Accept / Reject / Pending before it lands in your 2B. The auto-populated ITC table in GSTR-3B is hard-locked — you can no longer quietly edit the numbers at filing time; the fix has to happen upstream, in IMS and in your books. And Rule 88D lets the system compare the ITC you claimed in 3B against what 2B allows: cross the threshold and you receive a DRC-01C intimation — pay, explain, or your next GSTR-1 can be blocked.

ReconPe’s answer is to run the department’s comparison before the department does: IMS status is carried into every match verdict (Pending and Rejected invoices surface as actions, not matches), and the GSTR-3B tie-out computes the 3B-vs-2B gap per tax head with a ready-to-file verdict.

How ReconPe handles your GST close

ITC at risk, in rupees, with a vendor chase-list

Every invoice booked but missing from 2B rolls up into an at-risk total and a per-supplier list — so you know exactly which vendors to chase, and for how much, before the filing deadline. ReconPe drafts the chase email per vendor; you review and send it.

The fee-GST credit sellers forget

Marketplaces charge GST on their own fees — commission, shipping, collection — and that's input credit too. ReconPe matches the GST charged on marketplace fees against the operator's invoices in your 2B, so fee-GST credit is claimed, not silently dropped.

Probable matches, flagged for a human

When an invoice almost matches — a mangled invoice number, a partial-data row — it's surfaced as a probable match for your review rather than silently paired or silently failed. Accept it and the ITC headline updates; reject it and it stays an exception.

IRN-first, amendment-aware matching

Matches on the e-invoice IRN when present, falls back to GSTIN + normalised invoice number + date, treats B2BA / CDNRA amendments as superseding their original, and signs credit notes so they reduce ITC the way they should.

Late-filed credit is deferred, not lost

Attach next month's 2B and an invoice your supplier filed late is reclassified as deferred — available next period — instead of being written off as a permanent loss.

GSTR-1 and a GSTR-3B tie-out before you file

Match your sales register to filed GSTR-1 to catch under-reported liability, then tie GSTR-3B to GSTR-1 + 2B for a pre-file confirmation — with a ready-to-file status and an Excel / PDF close pack.

The details that decide a GST reconciliation

Whether a reconciliation ties out or quietly leaks comes down to how the portal file is actually shaped. These are the specifics ReconPe handles because it reads the real GSTR-2B, not an idealised one.

Reads the portal JSON the way it is actually shaped

GSTR-2B is deeply nested — supplier → invoice → line items, plus credit notes, amendments, imports and reverse-charge flags. ReconPe explodes that into clean invoice rows instead of one row per supplier, so every invoice is matched, not just summarised.

Deterministic keys, with a tolerance band

Matching is GSTIN-grouped and keyed on the IRN first, then the normalised invoice number — with a small rupee / percentage tolerance on tax so rounding doesn't create phantom mismatches. No fuzzy guessing on a tax identifier.

IMS status carried through to the verdict

Invoices marked Pending or Rejected in IMS, and credit flagged ineligible, are surfaced as actions to take before the 2B locks — not buried in a matched pile.

Books stay flexible; the portal file stays canonical

Upload your purchase or sales register as Excel or CSV from Tally, Zoho or any ERP. An AI-assisted mapper proposes which columns are GSTIN, invoice number, date and tax — you confirm. The government JSON is parsed natively.

A worked example: the ITC you booked vs the ITC you can claim

Illustrative — one purchase invoice, matched between your books and the GSTR-2B the portal generated. The figures are examples; the blocked credit is the kind ReconPe surfaces before you file.

Invoice booked in your purchase register
INV/2026/0042
Taxable value
₹50,000.00
GST claimed in books (18%)
₹9,000.00
Found in your GSTR-2B?
No — supplier hasn't filed GSTR-1
ReconPe flags
₹9,000 ITC at risk · chase this supplier before the deadline

Claim it anyway and it’s recoverable by the department with interest under Rule 36(4). ReconPe rolls every booked-but-missing invoice into an at-risk total and a per-supplier chase-list — and if the supplier files late, next month’s 2B reclassifies it as deferred credit instead of a write-off.

The supplier-chase playbook

Finding blocked credit is half the job — recovering it is a workflow. This is the escalation that works, and where ReconPe does the heavy lifting versus where the judgement stays yours.

  1. 1

    Identify

    Get the per-supplier rollup: which vendors, how many invoices, how much tax at risk. ReconPe produces this as the chase-list, in the app and in the Excel/PDF close pack.

  2. 2

    Park

    Book the blocked credit as deferred in your books rather than claiming it — claiming ITC that isn't in 2B is recoverable with interest. (Accounting guidance, not something software does for you.)

  3. 3

    Chase

    Send each vendor a specific ask: these invoices, this period, please file or amend. ReconPe drafts the email per vendor with the invoice list attached — you review and send it from your own mailbox.

  4. 4

    Protect

    Repeat late filers are tagged from history — a vendor who has cost you credit for three periods running is a vendor to renegotiate payment terms with. Many teams add a GST-compliance clause holding a payment percentage until the invoice reflects in 2B.

  5. 5

    Recover or escalate

    If the supplier files late, attaching next month's 2B reclassifies the invoice as deferred credit — recovered, not written off. If they never file, you have documentation of the chase for your position.

Frequently asked

What is GSTR-2B reconciliation?

GSTR-2B is the GST portal's system-generated statement of the supplier invoices available to you for input tax credit in a given month. GSTR-2B reconciliation is the process of matching that statement against your own purchase register so you can claim every rupee of credit you are entitled to, and avoid claiming credit on invoices that aren't actually in 2B (which is recoverable by the tax authority with interest and penalty).

How do I reconcile GSTR-2B with my purchase register?

Download your GSTR-2B JSON from the GST portal (Returns Dashboard → open the return → Download → Generate JSON), export your purchase register from Tally/your ERP as Excel or CSV, and upload both to ReconPe. It matches each invoice by IRN or by supplier GSTIN + invoice number + date within a small tolerance, then shows you three things: invoices booked but missing from 2B (ITC at risk), invoices in 2B not yet booked (unclaimed), and value mismatches to review.

What is input tax credit (ITC) and why reconcile it?

ITC is the GST you paid on purchases that you can set off against the GST you owe on sales. You can only claim it on invoices present in your GSTR-2B (Rule 36(4) / Section 16(2)(aa)). Reconciling 2B against your books each month catches suppliers who haven't filed (blocking your credit), invoice-level filing errors, and duplicate or reversed entries — so you neither lose credit you're owed nor over-claim credit you can't support.

What happens if a supplier hasn't filed their invoice?

That invoice won't appear in your GSTR-2B, so the credit is blocked for the month. ReconPe flags it as ITC at risk and groups it under that supplier in a chase-list. If the supplier files late and the invoice shows up in a later 2B, attaching the next-period statement lets ReconPe reclassify it as deferred — credit you'll get next month rather than a permanent loss.

Does ReconPe handle GSTR-1 and GSTR-3B as well?

Yes. It matches your sales register against filed GSTR-1 to surface under-reported or extra entries on the outward side, and ties GSTR-3B out against GSTR-1 + GSTR-2B as a pre-file confirmation — with a ready-to-file status. The whole monthly close (ITC, sales, and the 3B tie-out) lives in one place, with an Excel or PDF export.

Is GST reconciliation free?

You get 3 GST reconciliations free after signing up — enough to run a full month's close (GSTR-2B ITC, GSTR-1 sales, and the 3B tie-out) and see the input tax credit you were missing. Paid plans add monthly volume: Starter includes 25 GST reconciliations a month and Growth 100, with unlimited on Enterprise.

What is the difference between GSTR-2A and GSTR-2B?

GSTR-2A is dynamic — it keeps changing as suppliers file and amend — while GSTR-2B is a static statement generated on the 14th of each month and then frozen. GSTR-2B is the legal basis for your ITC claim under Rule 36(4), carries eligible/ineligible flags and IMS status, and is the statement you should reconcile against. 2A is useful only as a trend or audit reference.

What is Rule 88D and a DRC-01C intimation?

Rule 88D lets the GST system automatically compare the ITC you claimed in GSTR-3B against what your GSTR-2B allows. If the excess crosses the notified threshold, you receive a DRC-01C intimation and must either pay the difference or explain it — and until you respond, your next GSTR-1 can be blocked. The practical defence is to run exactly that comparison yourself before filing: ReconPe's GSTR-3B tie-out computes the 3B-vs-2B gap per tax head with a ready-to-file verdict, so you see the mismatch before the department's system does.

Can I claim ITC if an invoice is not in my GSTR-2B?

No — under Rule 36(4) and Section 16(2)(aa), credit is available only for invoices appearing in GSTR-2B. Claiming it anyway is recoverable with interest and possible penalty. The right treatment is to defer the credit, chase the supplier to file, and claim it in the period it lands in 2B. ReconPe flags these invoices as ITC at risk and reclassifies them as deferred when they appear in a later 2B.

What is the last date to claim ITC for a financial year?

Under Section 16(4), ITC for invoices of a financial year must be claimed by 30 November of the following year or the filing of the annual return, whichever is earlier. Late-filed supplier invoices that surface in a later GSTR-2B are still claimable within that window — which is why tracking deferred credit month over month matters rather than writing it off.

Do brand scheme credit notes reduce my ITC?

Only tax credit notes do. Most dealer scheme settlements — QPS rebates, price protection, post-sale discounts — arrive as financial (commercial) credit notes, which carry no GST adjustment: your ITC stays intact and they never appear in GSTR-2B, so they must be tracked against the brand's statement instead. A tax credit note issued under Section 34 does reduce the original GST and requires a proportionate ITC reversal. If you are a multi-brand dealer, our dealer-side guide to GST on scheme credit notes covers the classification, CBIC 251/08/2025, and free scheme goods under Section 17(5)(h).

Does ReconPe support GSTR-9 annual return reconciliation?

Not yet. ReconPe covers the monthly close — GSTR-2B ITC matching, GSTR-1 sales matching, and the GSTR-3B tie-out — plus TCS/TDS triangulation for marketplace sellers. The monthly closes and their Excel exports give you clean period-wise workings to build the annual return from, but GSTR-9 itself is not automated today.

Riya in a charcoal blazer at her co-working desk, one hand raised in a 'wait' gesture, the other holding a printed GSTR-2B statement. A founder leans in from across the desk, pointing proudly at a laptop showing a draft GSTR-3B with 'ITC to claim: ₹14.0L' highlighted.
Finance Manga · EP08

The ITC you booked isn't the ITC you can claim

A founder is about to claim ₹14 lakh of input tax credit. Riya asks how much is actually in their GSTR-2B. The gap is ₹2.8 lakh — and the fix is a phone call, not a write-off.

Read

Learn more

Run your next GST close in minutes

3 free GST reconciliations after sign-up — enough to close a full month and see the input tax credit you were leaving on the table.

Start free