GSTR-9C FY 2025-26 at a Glance: Dates, Thresholds and What Is New

Before getting into tables, it helps to fix the outline in your head. The reconciliation statement is not a separate return with its own due date. Instead, Section 44 of the CGST Act treats it as part of the annual return package, and Rule 80(3) of the CGST Rules requires it from every registered person whose aggregate turnover for the year exceeds ₹5 crore.

What GSTR-9C is, and what it is not

GSTR-9C is a statement that reconciles three numbers in your audited annual financial statements (turnover, tax and input tax credit) with the same numbers declared in your filed GSTR-9. It used to be called the “GST audit report” because, until FY 2019-20, a Chartered Accountant or Cost Accountant had to audit the accounts and certify the form under the old Section 35(5).

However, the Finance Act 2021 omitted Section 35(5) and rewrote Section 44. With effect from 1 August 2021, the statement became self-certified. So when a client asks whether they need a “GST audit” for FY 2025-26, the precise answer is no. They need a self-certified reconciliation, which their own team or an adviser can prepare, but which the authorised signatory signs.

Why FY 2025-26 needs extra care

Three things make this year different. First, the GST rate rationalisation notified on 17 September 2025 took effect from 22 September 2025, so most businesses have supplies at old rates for roughly six months and at new rates for the rest of the year. Second, the GSTR-9 and GSTR-9C formats were restructured for FY 2024-25 onwards by Notification 13/2025-CT, which added e-commerce disclosures and a late fee table. Third, the three-year bar on filing now runs on the portal, so a missed annual return can no longer be filed “whenever”.

Who Must File GSTR-9C for FY 2025-26

The threshold sounds simple, yet most applicability mistakes come from measuring the wrong turnover. The test uses aggregate turnover as defined in Section 2(6) of the CGST Act: the value of all taxable supplies, exempt supplies, exports and inter-State supplies of persons having the same PAN, computed on an all-India basis. It excludes the tax itself and inward supplies taxed under reverse charge.

In other words, you add up every GSTIN under the PAN. If that combined figure crosses ₹5 crore, GSTR-9C FY 2025-26 applies and each GSTIN files its own GSTR-9C, including a branch registration whose own sales are small.

The three turnover tiers

Notably, Notification 15/2025-CT is worded for “financial year 2024-25 onwards”, so the ₹2 crore exemption from GSTR-9 no longer depends on a fresh notification each year. It does not, however, change the ₹5 crore trigger for the reconciliation statement.

Who never files GSTR-9C

The annual return provisions exclude certain registrations altogether. Accordingly, the following persons do not file GSTR-9 or GSTR-9C regardless of turnover:

• Composition taxpayers (they file GSTR-4 as their annual return)
• Input Service Distributors
• Casual taxable persons and non-resident taxable persons
• Persons deducting tax under Section 51 or collecting tax under Section 52
• Suppliers of online information and database access services located outside India

Inside the Form: How GSTR-9C Is Structured

Once you know you must file GSTR-9C FY 2025-26, the next question is what the form wants from you. GSTR-9C has two parts. Part A is the reconciliation statement itself, divided into five sub-parts. Part B is the self-certification by the authorised signatory, which replaced the old auditor’s certificate.

What auto-fills and what you type

Several “as per GSTR-9” fields auto-populate from the annual return you have already filed: turnover in Table 5Q, taxable turnover in Table 7F, tax payable in Table 9Q and ITC in Table 12E. By contrast, every “as per books” figure is yours to enter, which is exactly why GSTR-9C carries weight. It forces the person signing Part B to put the audited number next to the return number and explain the gap.

For that reason, the portal unlocks GSTR-9C only after GSTR-9 is filed. You can still prepare GSTR-9C offline earlier, but you cannot submit it first.

Turnover Reconciliation in GSTR-9C FY 2025-26: Tables 5 to 8 Worked Through

Table 5 is where most reviewers start, and it is where weak workings show up first. The table begins with turnover per audited accounts for the State (Table 5A), adds or deducts specific timing and definitional differences, and arrives at “annual turnover after adjustments” (Table 5P). That figure is then compared with turnover declared in GSTR-9 (Table 5Q), and any balance is “unreconciled turnover” (Table 5R).

The adjustment rows you will actually use

• 5B (+) Unbilled revenue at the beginning of the year: booked last year, invoiced this year
• 5C (+) Unadjusted advances at the end of the year: tax paid on advances for services, revenue not yet booked
• 5D (+) Deemed supply under Schedule I: stock transfers to your own GSTINs in other States, which books eliminate
• 5E (−) Credit notes issued after the year end but reflected in the annual return
• 5F and 5J (+) Trade discounts and credit notes that reduce book revenue but are not permissible under GST
• 5H (−) Unbilled revenue at the end of the year
• 5I (−) Unadjusted advances at the beginning of the year
• 5N (±) Foreign exchange fluctuation, and 5O (±) any other adjustment, explained

Worked example: a two-State manufacturer

Consider a polymer products company with a factory in Maharashtra and a depot in Gujarat. Its audited revenue is first allocated between the two GSTINs. For the Maharashtra GSTIN, the Table 5 working looks like this:

The ₹4.50 lakh gap is not automatically a problem. Here, it came from an invoice dated 31 March 2026 that the books recorded on 1 April 2026, a cut-off difference. Since the higher figure is in GSTR-9, tax has already been paid, and the explanation goes in Table 6. Had the gap run the other way, with books higher than the return, you would have to check whether tax was short-paid.

Allocating audited accounts across GSTINs

Audited financial statements are prepared for the entity, while GSTR-9C is filed per GSTIN. Therefore, the first working for any multi-State business is a GSTIN-wise allocation of revenue, usually from the sales ledger’s branch tagging. Keep that allocation schedule with your papers; it is the single document that explains why each State’s Table 5A adds up to the audited total.

From gross to taxable turnover: Table 7

Table 7 takes the adjusted turnover from 5P and strips out what is not taxable at your end: exempt, nil-rated, non-GST and “no supply” turnover (7B), zero-rated supplies without payment of tax (7C), supplies on which the recipient pays under reverse charge (7D), and supplies on which an e-commerce operator pays tax under Section 9(5) (7D1, added by Notification 13/2025-CT). The result (7E) is compared with taxable turnover in GSTR-9 (7F). Unexplained differences here are more sensitive than in Table 5, because they point directly at tax.

The 22 September 2025 Rate Split: Reconciling Tax Paid in Table 9

Table 9 asks for your outward tax liability rate by rate, as per books, and compares the total with tax payable as declared in GSTR-9. In a normal year that is a summary exercise. For GSTR-9C FY 2025-26, however, many product lines sit at two rates, because the earlier slabs applied up to 21 September 2025 and the rationalised structure applied from 22 September 2025.

Splitting the year cleanly

Take a Pune-based distributor of air-conditioners and accessories. Air-conditioners moved from 28% to 18% under the rationalisation, while accessories stayed at 18%. Its rate-wise working for Table 9 looks like this:

The 28% value goes in the 28% row and the post-change value joins the accessories in the 18% row. If the 18% row in GSTR-9C does not match the sum of GSTR-1 data at 18%, the usual culprit is a billing system that switched rates a few days early or late.

Invoices that straddle the change date

Where supply, invoice and payment fall on different sides of 22 September 2025, Section 14 of the CGST Act decides the rate. In broad terms, if two of the three events (supply, invoice, receipt of payment) occurred on or after the change, the new rate applies; if two occurred before it, the old rate applies. For example, an advance of ₹25 lakh received on 15 September 2025 against ACs delivered and invoiced on 25 September 2025 attracts 18%, because both the supply and the invoice came after the change.

Likewise, a credit note issued in December 2025 against a July 2025 invoice must reverse tax at the rate charged on the original invoice. Mixing these up is the most common reason Table 9 refuses to tie.

Where a new rate has no row of its own

The rate rows in Table 9 still list the legacy slabs (5%, 12%, 18%, 28%, 3%, 0.25% and 0.10%, with reverse charge variants) plus an “Others” row (9K1). Supplies at the new 40% rate therefore have no dedicated row in the form as amended by Notification 13/2025-CT. Report them in the “Others” row unless the FY 2025-26 offline utility adds a specific line, and keep a note in Table 10 explaining what that row contains.

ITC Reconciliation: Tables 12 to 16

In GSTR-9C FY 2025-26, Part IV compares input tax credit in your books with what you availed in GSTR-9. Table 12 starts from ITC per audited accounts (12A), adds ITC booked in an earlier year but claimed this year (12B), deducts ITC booked this year that will be claimed in a later year (12C), and arrives at the books figure (12D). That is then compared with the ITC availed as per GSTR-9 (12E, auto-filled from Table 7J of GSTR-9). The difference is 12F, explained in Table 13.

The 30 November 2026 cut-off

For FY 2025-26 invoices and debit notes, Section 16(4) allows credit only up to 30 November 2026 or the date you file the GSTR-9, whichever is earlier. Any eligible credit in your books that you fail to claim by then is lost. It will show up as a 12F difference that you can explain but cannot claim through GSTR-9C. Consequently, finishing the ITC reconciliation before November returns is far more valuable than doing it in December.

Similarly, credit on invoices that suppliers uploaded late, or that you kept pending in the Invoice Management System, needs a decision before the cut-off. Our guide to reconciling GSTR-2B with your purchase register explains a practical matching method.

Expense-wise ITC: Table 14

Table 14 maps ITC to expense heads such as purchases, freight, power and fuel, rent, insurance and capital goods, and compares the total with GSTR-9. In recent years this table has been optional for self-certified statements, and the FY 2024-25 form kept it so. Check the FY 2025-26 utility before you decide to skip it, and remember that completing it voluntarily is often the fastest way to spot blocked credit under Section 17(5) hiding in an expense ledger.

When the difference becomes tax

If the reconciliation shows ITC availed in returns that the books do not support, the excess is payable along with interest under Section 50. Table 16 records the tax payable on such unreconciled ITC, and the amount is discharged through Form DRC-03.

How to File GSTR-9C FY 2025-26 on the GST Portal: 7 Steps

With the workings in hand, filing GSTR-9C FY 2025-26 is a short sequence. The GSTR-9/9C tile appears only after every GSTR-1 and GSTR-3B for FY 2025-26 has been filed for that GSTIN, as GSTN’s advisory of 13 October 2026 reminds taxpayers.

1. Confirm applicability and prerequisites. Recheck PAN-level aggregate turnover for FY 2025-26, confirm all GSTR-1 and GSTR-3B returns are filed, and keep the audited financial statements and GSTIN-wise allocation ready.
2. Finish corrections by 30 November 2026. Claim remaining eligible ITC, issue pending credit notes and fix GSTR-1 or GSTR-3B errors in returns filed up to that date, so that GSTR-9 and GSTR-9C start from the cleanest possible base.
3. Pay any shortfall through DRC-03. Where your workings show short-paid tax, pay it with interest under Section 50 through Form DRC-03 before filing, choosing the annual return as the cause of payment.
4. File GSTR-9 first. Prepare GSTR-9 online or offline, review the system-computed draft, and file it with DSC or EVC. GSTR-9C cannot be submitted until this is done.
5. Prepare GSTR-9C in the offline tool. Download the GSTR-9C offline utility from the portal, import the GSTR-9 data, enter the books figures for Tables 5, 7, 9, 12 and 14 (if you choose), and write clear reasons in Tables 6, 8, 10 and 13.
6. Upload, validate and review the PDF. Generate the JSON, upload it on the GSTR-9C tile, resolve any error report, and read the generated draft line by line before signing.
7. Self-certify and file. Attach the audited financial statements where the portal asks, sign Part B with DSC (mandatory for companies and LLPs) or EVC, file, and save the ARN with your reconciliation papers.

If you prefer to see the portal screens, the walkthrough below shows a live GSTR-9C filing using the offline utility. The interface for FY 2025-26 may differ slightly from the recording, so follow the current utility where they diverge.

GSTR-9C FY 2025-26 Late Fee, Additional Liability and the Three-Year Bar

Missing the deadline is costly in more than one way. The late fee itself is modest for most businesses, but it runs every day, and the law now puts an outer limit on how late you can file at all.

How the late fee works when GSTR-9C is delayed

Section 47(2) levies a late fee for failing to furnish the annual return under Section 44 by the due date. CBIC Circular No. 246/03/2025-GST (30 January 2025) clarified that where GSTR-9C is required, the annual return is complete only when both GSTR-9 and GSTR-9C are filed. In practice, filing GSTR-9 on time and GSTR-9C late still attracts a late fee, counted from the due date up to the date GSTR-9C is filed. The amnesty in Notification 08/2025-CT covered only years up to FY 2022-23, so it does not help for FY 2025-26.

Worked example: A company with ₹12 crore of turnover files GSTR-9 on 28 December 2026 but GSTR-9C only on 10 February 2027. The delay is 41 days (1 January to 10 February). The fee is ₹100 × 41 = ₹4,100 (₹2,050 CGST and ₹2,050 SGST), well within the cap of 0.04% of ₹12 crore, which is ₹48,000. The new Table 17 of GSTR-9C records this late fee payable and paid.

Additional liability from the reconciliation

Where Tables 9 to 11 or 12 to 16 reveal tax that should have been paid, GSTR-9C does not wipe it away; it records it. The amount, with interest, is paid through DRC-03, and the reference is reported in the form. Paying voluntarily before any notice is usually the cheapest route, because proceedings under Section 73 or 74A add penalty on top of tax and interest.

The three-year bar: 31 December 2029

The Finance Act 2023 inserted a time limit in Section 44, in force from 1 October 2023 through Notification 28/2023-CT: an annual return cannot be furnished after three years from its due date. GSTN has been enforcing this on the portal since 2025, and its advisories specifically list GSTR-9 and GSTR-9C. For FY 2025-26, the window therefore closes on 31 December 2029. After that, the return cannot be filed at all, and the non-filing becomes a matter for assessment.

6 GSTR-9C FY 2025-26 Mistakes and Two Client Scenarios

Most notices that follow a reconciliation statement trace back to a handful of avoidable errors. Before you sign Part B of your GSTR-9C FY 2025-26, run through this list.

1. Using GSTIN turnover instead of PAN turnover for applicability. A small branch GSTIN under a ₹5 crore-plus PAN still files GSTR-9C.
2. Typing GSTR-9 figures into the “as per books” columns. The form is meaningless if both columns come from returns; reviewers notice zero differences on every line of a large business.
3. Ignoring the rate split. Reporting full-year sales of a product at its post-September rate makes Table 9 look short-paid or over-paid when it is neither.
4. Leaving reasons blank or generic. “Difference due to timing” is not an explanation. Name the item, the amount and the table where it is accounted for.
5. Treating GSTR-9C as a second chance to claim ITC. Credit not availed by 30 November 2026 cannot be claimed through the reconciliation; it only gets disclosed.
6. Filing GSTR-9 and forgetting GSTR-9C. Under Circular 246/03/2025-GST, the annual return remains incomplete, and the late fee keeps running, until the reconciliation statement is filed.

Scenario 1: the branch that forgot it was a “large taxpayer”

A Coimbatore textile exporter with a Tamil Nadu GSTIN (₹14 crore turnover) also holds a Karnataka GSTIN for a showroom (₹1.2 crore). The finance team filed GSTR-9C only for Tamil Nadu. When the Karnataka officer noticed GSTR-9 without GSTR-9C, the business had to file it late and pay the late fee for the gap. The fix is simple: build a PAN-level applicability check into the year-end calendar, so every GSTIN is flagged together.

Scenario 2: the ₹18 lakh “difference” that was not tax

A Hyderabad software company found that its audited revenue exceeded GSTR-9 turnover by ₹18 lakh. On investigation, ₹11 lakh was unbilled revenue recognised under the revenue accounting standard at 31 March 2026 (Table 5H) and ₹7 lakh was foreign exchange gain on export receivables (Table 5N). Neither was a supply on which tax had been missed. With both items placed in their proper rows, Table 5R fell to nil and no DRC-03 was needed.

Key Takeaways

• GSTR-9C FY 2025-26 is required where PAN-level aggregate turnover exceeds ₹5 crore, and each GSTIN under that PAN files its own statement.
• It is self-certified since 1 August 2021; no CA or CMA certificate is required, but the signatory owns every number.
• The due date is 31 December 2026, and GSTR-9C can be submitted only after GSTR-9.
• Claim ITC and fix outward errors by 30 November 2026; GSTR-9C can disclose differences but cannot correct them.
• Split sales at 21/22 September 2025 for Table 9, and apply Section 14 to invoices that straddle the change.
• Late fee runs until the complete annual return, including GSTR-9C, is filed (Circular 246/03/2025-GST).
• Filing is barred after 31 December 2029 under the three-year rule in Section 44.

Frequently Asked Questions on GSTR-9C FY 2025-26

Conclusion: Start the GSTR-9C FY 2025-26 Workings Now

A reconciliation statement is only as good as the schedules behind it. For GSTR-9C FY 2025-26, that means a GSTIN-wise allocation of audited revenue, a Table 5 bridge with every adjustment named, a rate-wise liability split at 22 September 2025, and an ITC reconciliation finished before the 30 November 2026 cut-off. Do those four things and the portal steps take an afternoon. Leave them to the last week of December and the form becomes a list of differences you cannot fix.

As a next step, run your purchase data through the free GST ITC reconciliation tool, then read the official GST portal user manuals for the current offline utility. For the underlying rules, the CBIC circular on GSTR-9C late fee and the CGST Rules on the CBIC GST website are the primary sources. More guides on returns, credit and notices are collected in our GST topic hub.