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Reconcile every purchase document in your books with the correct GST Portal statement before preparing GSTR-3B. The practical sequence is to download the period’s GSTR-2B, match supplier and invoice-level fields, investigate exceptions, review Invoice Management System (IMS) actions, assess statutory eligibility separately, and then map the reviewed result to GSTR-3B. Matching reduces avoidable delays and duplicate claims, but a match by itself does not prove that input tax credit (ITC) is legally available.
The process below is designed for Indian GST-registered businesses and their accounts-payable, tax and finance teams. Portal labels and return-period rules can change, so use the current guidance for the period being filed.
What you are reconciling: your books, GSTR-2B and GSTR-3B
GSTR-2B is a static, read-only statement generated from supplier and other source filings. It is not a return that the recipient files. The GST Portal makes it available for viewing and download in Excel or JSON. Its inputs include supplier-reported B2B documents, specified Input Service Distributor data and import-of-goods IGST data received from ICEGATE. The statement separates indicated available credit, reversal information and listed unavailable cases.
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The GST Portal’s own instruction is direct: “Taxpayers are advised to ensure that the data generated in Form GSTR-2B is reconciled with their own records and books of accounts.” Read the full GST Portal FAQ on viewing Form GSTR-2B for the current generation and download behavior.
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Think of the three records as serving different purposes:
| Record | What it represents | How your team should use it |
|---|---|---|
| Purchase register and books | What your business ordered, received, recorded and paid or owes | Primary evidence for document identity, accounting treatment, business purpose and tax coding |
| GSTR-2B | What suppliers and specified systems reported for the relevant statement period | External confirmation to compare against the ledger and to identify reported, amended, reversed or unavailable entries |
| GSTR-3B | The return in which the taxpayer reports eligible ITC, reversals and other tax figures | Final filing output after document matching and a separate eligibility review |
A portal availability indicator does not settle every legal condition. The system identifies specified unavailability scenarios, while the taxpayer must self-assess other restrictions and reverse ineligible credit.
Set up a controlled period file
Collect all source records
At each monthly or quarterly close, create one folder or electronic workpaper for the filing period. Export the purchase register or accounts-payable ledger, supplier invoices, debit notes, credit notes, amendments, import documentation where relevant and the period’s GSTR-2B. Download GSTR-2B in Excel or JSON from the GST Portal and retain the original file without editing it.
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Select the statement period correctly
Use the GSTR-2B period generated under the Portal’s process for the comparison, not simply the invoice date. Supplier filing dates, amendments and document types affect when an item appears. Record the exact return period and the download date in the workpaper. If a supplier says an invoice was filed but it is absent, compare the supplier’s filing period and amendment details before concluding that the filing is missing.
Lock a baseline before matching
Save a read-only copy of the ledger extract and note its row count and total taxable value and tax by tax type. If the ledger is refreshed later, label the new extract with its extraction time and preparer. This prevents a changed spreadsheet from silently replacing the figures used for the GSTR-3B review.
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Match at document level, not only by total
Start with a unique key made from supplier GSTIN, document type, document number and document date. Then compare the amounts and place-of-supply fields. Do not treat a total that happens to agree as evidence that every underlying document agrees.
| Field | Check in your books | Check in GSTR-2B | Typical response to a difference |
|---|---|---|---|
| Supplier GSTIN and legal name | GSTIN on the invoice and vendor master | GSTIN reported by the supplier | Verify the invoice, master data and whether the supplier used the correct registration |
| Invoice, debit-note or credit-note number | Exact identifier captured from the document | Identifier transmitted in the supplier filing | Check leading zeroes, spaces, punctuation, truncation and amended identifiers |
| Document date and type | Invoice or note date and whether it is a debit or credit note | Reported date and document category | Determine whether the item belongs to another statement period or is an amendment |
| Taxable value | Net taxable amount after commercial adjustments | Supplier-reported taxable value | Compare line-level tax coding and ask the supplier to amend if the reported value is wrong |
| IGST, CGST and SGST amounts | Tax booked and split by type | Tax amounts reported in the statement | Investigate rounding, tax-rate, amendment and credit-note effects |
| Place of supply | Place shown on the invoice and transaction facts | Place reported in the filing | Resolve state or supply-type differences before deciding the tax treatment |
| Amendment and original-document references | Links between the current document and the original entry | Amendment or note references reported by the supplier | Prevent the original and amended value from both being claimed |
Invoice-number capture differences and tax-amount or place-of-supply mismatches are specifically identified as reconciliation concerns in the Invoice Registration Portal’s guidance on e-invoicing, ITC claims and reconciliation blind spots. Treat every difference as an exception to investigate, not as automatic entitlement or automatic denial.
Classify exceptions so they can be cleared
Use one exception log for the period. Assign an owner and a due date to each line; otherwise unresolved items tend to reappear at filing time without a decision.
- Supplier filing absent: the invoice is in your books but no corresponding document appears in the selected GSTR-2B.
- Identifier or GSTIN mismatch: the supplier, document number, date or document type differs enough to prevent a reliable match.
- Value or tax mismatch: taxable value, IGST, CGST or SGST differs from the invoice or ledger.
- Credit-note or amendment mismatch: a note or amended invoice is missing, duplicated or not linked to its original.
- Place-of-supply or eligibility concern: the reported state, supply classification or transaction facts require tax or legal review.
- Duplicate or already-reversed credit: the same document was imported twice, claimed in an earlier period or reversed previously.
Minimum log fields are supplier GSTIN and name, document number and date, statement period, exception category, taxable value and tax at risk, assigned owner, supplier-contact date, requested correction, IMS decision, eligibility decision and final resolution. Keep the original evidence or a file link beside each entry.
Review IMS actions before relying on records
Where the Invoice Management System presents records for action, compare each relevant record with the invoice and your ledger before selecting accept, reject or pending. An accepted record should still be checked for duplicate booking, credit notes and statutory restrictions; a rejected record should have a documented reason and supplier follow-up.
The GST Portal’s FAQ for the October 2025 changes says that, for specified records, a pending action can remain for one tax period. After the specified window ends, pending action is disabled and inaction can be treated as deemed acceptance. Apply the rule for the record type and period shown in the Portal’s current IMS changes FAQ; do not carry a pending item indefinitely as a substitute for a decision.
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Ask suppliers for corrections with a traceable request
Contact the supplier as soon as an exception is confirmed. Send a short issue list rather than a general request to “check GST.” Identify your GSTIN, the supplier GSTIN, document number and date, the value and tax in your books, the value and tax reported, the statement period, and the correction or amendment needed. Attach the invoice or a secure reference and state the date by which you need confirmation for the filing calendar.
Record whether the supplier has filed, amended or merely promised to file. Do not move an item into eligible ITC solely because a supplier says it will be corrected. Re-run the comparison after the relevant filing or amendment appears in GSTR-2B and close the exception only when the document, amounts and treatment agree.
E-invoicing can reduce manual capture. The Invoice Registration Portal explains the e-invoicing mandate and data flow; registered invoice data is shared with the GST system, and relevant details can populate the supplier’s GSTR-1 and the buyer’s GSTR-2B. Automation reduces keying errors but does not replace reconciliation to the purchase ledger or the eligibility review.
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After matching, review whether each candidate credit satisfies the conditions applicable to the taxpayer, transaction and period. GSTR-2B flags only specified unavailable cases. The Portal cautions that other legal restrictions may apply and that taxpayers must self-assess and reverse ineligible credit.
- Confirm that the purchase relates to business activity and that the tax document is valid and addressed to the correct GST registration.
- Check receipt of the goods or services and the accounting treatment, including capitalisation or expense classification where relevant.
- Review blocked-credit categories, exempt or non-business use, employee or personal consumption and any required proportionate reversal.
- Check credit notes, discounts, returns and other events that reduce the eligible amount.
- Review reverse-charge transactions separately; do not expect a supplier-reported B2B invoice to represent the recipient’s reverse-charge liability.
- Verify the applicable time limit and Section 16(4) or other statutory conditions for the particular tax period against current law. Do not apply a generic cutoff copied from an older period.
Document the conclusion as eligible, ineligible, partially eligible or unresolved, with the rule or fact supporting the decision. A document that matches perfectly can still require reversal; a document that is temporarily absent can require follow-up rather than an automatic permanent denial.
Map the reviewed result to GSTR-3B
Use the reconciled document list to review the system-generated GSTR-3B summary. The Portal’s GSTR-2B guidance includes a section mapping GSTR-2B figures to GSTR-3B; use that mapping for the current return period and then verify each adjustment.
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| Reconciled item | GSTR-3B treatment | Control to perform |
|---|---|---|
| Eligible inward-supply ITC | Enter in the appropriate eligible ITC field by tax type | Agree the field total to the approved document-level schedule |
| Ineligible or blocked credit | Exclude or reverse in the applicable reversal field | Retain the reason and calculation for each reversal category |
| Credit notes and supplier amendments | Reduce or adjust the related ITC as applicable | Ensure the original and amended entries are not both counted |
| Reverse-charge inward supplies | Report tax and eligible credit in the relevant reverse-charge fields after payment and eligibility review | Reconcile to the reverse-charge register and payment records |
| IMS or other unavailable records | Do not include until the reviewed status and legal treatment support the claim | Keep the pending, rejected or deemed-accepted decision with the period workpaper |
Compare the auto-populated values with your reviewed schedule. If you edit a system-populated figure, record the reason and retain the supporting calculation. Perform a duplicate check across current-period invoices, prior-period claims, amendments and credit notes before submitting GSTR-3B.
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The GST Portal’s GSTR-1 guide lists online entry, the Returns Offline Tool and third-party ASP applications through GSPs as preparation modes. These channels can help suppliers submit data, but your recipient-side control remains the same: obtain the source document, compare it with GSTR-2B and review eligibility.
For higher volumes, an accounting or reconciliation system can automate file imports, fuzzy matching and exception assignment. Configure it to preserve the supplier GSTIN, original and amended document numbers, tax components, statement period and status history. Automation should surface uncertain matches for human review rather than silently forcing them into an eligible bucket.
Independent reader supportYour contribution helps us test, update, and keep practical guides available for everyone.Maintain a period workpaper that another reviewer can reproduce
Keep the following together for each filing period:
- Original GSTR-2B Excel or JSON download and the recorded statement period.
- Purchase-register and accounts-payable extracts used for the comparison.
- Invoice, debit-note, credit-note, amendment and import support for material items.
- Exception log showing owner, supplier communication, correction status and closure date.
- IMS accept, reject or pending decisions and the rationale for each non-obvious action.
- Eligibility review, blocked-credit calculations and reversal workings.
- Final document-level schedule tied to the GSTR-3B fields and any edited auto-populated values.
- Reviewer sign-off and the date of submission.
Use versioned filenames such as GSTIN_period_GSTR2B_original, GSTIN_period_exception_log_v2 and GSTIN_period_GSTR3B_final. Restrict editing rights on the original download and keep an audit trail for changes to the approved schedule.
Troubleshoot the common mismatch patterns
An invoice is in the ledger but absent from GSTR-2B
Verify that you selected the correct statement period, that the supplier used your GSTIN and that the document was actually filed rather than only generated in an invoicing system. Ask for the supplier’s filing or amendment reference, keep the item in the exception log and reassess it when a later statement includes it. Do not claim it merely because the invoice is genuine in your books.
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The invoice number differs by punctuation or zeroes
Compare the original PDF or e-invoice data with the supplier’s reported identifier. Preserve the exact reported number in the matching table and create a controlled alias only if your accounting system needs one. Never use a broad fuzzy match that could combine two invoices from the same supplier.
Tax amount or place of supply is different
Recalculate tax from the taxable value and rate, check whether a credit note or amendment changed the entry, and verify the state registration and supply facts. Escalate to the tax reviewer when the difference changes IGST versus CGST and SGST or affects eligibility. Request supplier correction when the filed data is wrong.
A credit note appears after the original invoice was claimed
Link the note to the original document, quantify the reduction and identify the period in which the adjustment must be reflected. Block a second claim of the original amount and update both the exception log and the GSTR-3B working.
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Check whether one line is an amendment, an import duplicate or a repeated upload. Compare document identifiers, supplier GSTIN, tax amounts and original-document references. Keep one approved record and mark the duplicate as excluded with a reason.
The system says credit is available but the reviewer finds a restriction
Record the legal or factual reason for exclusion or reversal. GSTR-2B is a reconciliation aid, not a statutory eligibility certificate; the taxpayer’s documented self-assessment controls the filing decision.
Quick Recap
A practical close calendar
- Day 1–3 after books close: lock the purchase register, collect invoices and notes, and download the applicable GSTR-2B.
- Day 3–7: run the document-level match, classify exceptions and assign owners.
- Before supplier filing cut-offs: send confirmed discrepancy lists and capture supplier responses.
- Before IMS action closes: review each relevant record and make the required accept, reject or pending decision under the current period rules.
- Before GSTR-3B preparation: complete the separate eligibility review, calculate reversals and isolate reverse-charge items.
- During return preparation: map the approved schedule to GSTR-3B, investigate differences from auto-populated values and run the duplicate check.
- After filing: freeze the final workpaper, record reviewer sign-off and carry only documented unresolved items into the next period.
Controls that prevent avoidable ITC delays
- Set a materiality threshold for escalation, but do not ignore small duplicate or blocked credits that can accumulate across periods.
- Separate the person who prepares the match from the person who approves eligibility and GSTR-3B mapping.
- Use a supplier scorecard based on recurring missing filings, identifier errors and correction turnaround, without treating the score as proof of any individual invoice’s eligibility.
- Reconcile tax-type totals and document counts, not only the grand total.
- Carry forward unresolved exceptions with their original period, rather than re-dating them to the current month.
- Review Portal guidance for each filing period because IMS behavior, statement generation and statutory deadlines may change.
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