One GSTR-9, Two Rate Regimes: Splitting FY 2025-26 Data at the 22 September 2025 Rate Change
By GST Reco Pro
GST Reco Pro builds browser-based tools for GST and TDS reconciliation, used by Chartered Accountants and corporate tax teams across India.
FY 2025-26 is the first annual return that spans GST 2.0. Supplies before 22 September 2025 carry the old 12%/28% slabs and compensation cess; supplies after carry the 5%/18%/40% structure. Here is how to split a year of return data cleanly before GSTR-9 and GSTR-9C are due on 31 December 2026.
Every annual return has a reconciliation problem. The FY 2025-26 return has a second one on top: the GST 2.0 rate restructuring took effect on 22 September 2025, almost exactly halfway through the year. For the first five and a half months, supplies were taxed under the old four-slab structure with compensation cess on many goods. For the remaining six and a half, they were taxed under the 5%, 18% and 40% structure, with cess removed on nearly everything except tobacco products.
GSTR-9 and GSTR-9C for FY 2025-26 are due on 31 December 2026. GSTR-9 is mandatory where aggregate turnover exceeds ₹2 crore, and GSTR-9C applies above ₹5 crore. Both have to describe that year as one set of numbers, and the place this goes wrong is almost always the boundary.
Where the two regimes show up in the return
The summary tables of GSTR-9 — outward supplies, ITC, tax paid — are organised by the nature of the supply and the tax head, not by rate. A rate change does not add rows to them. The two regimes become visible in three places instead:
- The HSN summaries. Table 17 (outward) and Table 18 (inward) report HSN-wise values with the rate. An item whose rate changed on 22 September appears twice: once at its old rate and once at its new one.
- The cess columns. Compensation cess appears for the pre-change months on most goods that carried it, and should be nil or close to it afterwards except for tobacco-related goods. A cess figure that does not drop after September is a red flag.
- The GSTR-9C reconciliation. Turnover and tax as per audited books are compared with the returns. If the books apply the new rate to a pre-22 September invoice, or the reverse, the tax reconciliation will not close.
A workflow for splitting the year
- Put all twelve months side by side. Convert the year's GSTR-1 and GSTR-3B returns into one workbook, one row per month, so that tax by head can be summed across any range of months, not just the full year.
- Draw the boundary at 22 September 2025. April to August 2025 is entirely old regime. October 2025 to March 2026 is entirely new regime. September is mixed, and is the only month you need to split.
- Split September by invoice date. Use the sales register to separate invoices dated 1 to 21 September from those dated 22 to 30 September, and check that each part ties to the rate-wise lines in September's GSTR-1 HSN summary.
- Rebuild the HSN tables rate by rate. Combine the twelve GSTR-1 HSN summaries into a single annual list keyed on HSN and rate. An HSN that appears at both its old and new rate is expected; an HSN that still appears at a removed rate (12% or 28%) after September needs explaining.
- Trace credit notes back to the original invoice. A credit note issued after 22 September against an invoice from before it reverses tax at the rate charged on the original invoice, not at the new rate. Check these individually; they are where most cross-regime differences come from.
- Reconcile cess separately. Total the cess paid for April to September 2025 and confirm it falls away afterwards for anything other than tobacco products. Any unused cess credit left in the ledger needs a separate decision.
- Then reconcile to the audited books. Only once the return-side figures are split cleanly does the GSTR-9C comparison with the financial statements become meaningful.
Changes to the forms themselves
Separately from the rate change, the GSTR-9 and GSTR-9C formats were revised by CBIC notifications in 2025, including changes reported to tie ITC tables more closely to GSTR-2B and the Invoice Management System. The exact table-level changes for FY 2025-26 should be read from the notified forms and the GSTN advisories themselves, not from secondary summaries, which do not always agree.
Do not file GSTR-9 before your ITC is final
Under Section 16(4), ITC for FY 2025-26 can be claimed only until the earlier of 30 November 2026 or the date GSTR-9 for the year is filed. Filing the annual return in, say, October ends the ITC window early. Finish claiming every pending FY 2025-26 credit first, then file.
The workflow above starts with twelve months of returns in one sheet. GST Reco Pro converts GSTR-1 and GSTR-3B PDFs into a single month-by-month Excel workbook, entirely in your browser, so drawing the 22 September boundary is a formula rather than a re-keying exercise.
Convert a year of GSTR returns to Excel →Background reading: what the GST 2.0 slab structure changed and why it created a reconciliation boundary.
Read the GST 2.0 rate guide →Related reading: the general GSTR-9 and GSTR-9C pre-filing checklist.
Read the annual return checklist →Frequently Asked Questions
What is the due date for GSTR-9 and GSTR-9C for FY 2025-26?
31 December 2026. GSTR-9C is filed along with GSTR-9 and has no separate due date. Check the GST portal for any extension notified by CBIC.
Do I need to report the old and new GST rates separately in GSTR-9?
The summary tables of GSTR-9 are not organised by rate, so the rate change does not add rows to them. It shows up in the HSN summaries in Tables 17 and 18, which report values with the rate, so an item whose rate changed on 22 September 2025 will appear at both its old and new rate.
How do I split September 2025, which spans both rate regimes?
GSTR-3B does not show rates, so use the September GSTR-1 HSN summary, which reports values by rate, and cross-check it against the sales register split by invoice date: 1 to 21 September under the old rates and 22 to 30 September under the new ones.
At what rate is a credit note issued after 22 September 2025 reported?
A credit note reverses tax at the rate charged on the original invoice. If the original invoice was issued before 22 September 2025 at an old rate, the credit note reverses tax at that old rate, even though it is issued after the change.
Does filing GSTR-9 early affect my input tax credit?
Yes. Under Section 16(4), ITC for FY 2025-26 can be claimed only until the earlier of 30 November 2026 or the date GSTR-9 for that year is filed. Filing the annual return early closes the ITC window early.