Businesses registered under GST must understand their annual return filing obligations to maintain compliance and report their financial transactions accurately. GSTR-9 is the annual return filed by eligible registered taxpayers, while GSTR-9C is a reconciliation statement required for specified taxpayers when applicable under GST law. Eligibility depends on factors such as the financial year, aggregate turnover and applicable exemptions or notifications. Whether you completed your GST registration online recently or have been managing GST compliance for several years, understanding these requirements can help you determine which annual filings apply to your business and prepare the necessary records before the due date.
Quick Summary
GSTR-1 records the outward supplies reported by a business, while GSTR-3B is used to declare the corresponding tax liability and pay the tax due. When the liability reported in these returns does not match, the GST system may identify the difference and issue an intimation under Rule 88C. The taxpayer may then need to pay the differential tax and applicable interest or provide an explanation within the prescribed time. Repeated or unexplained differences can also increase the risk of further scrutiny and compliance action.
- GSTR-1 vs GSTR-3B: Differences between the outward tax liability reported in GSTR-1/IFF and the liability declared in GSTR-3B can trigger a Rule 88C intimation when the prescribed conditions are met.
- DRC-01B: A taxpayer receiving a Rule 88C intimation generally has 7 days to pay the differential amount with applicable interest or submit an explanation.
- Auto-population: GST return systems have introduced greater auto-population of liability figures from GSTR-1 into GSTR-3B, reducing the scope for inconsistent reporting.
- Filing restrictions: Non-compliance with applicable return-filing requirements can result in restrictions on subsequent GST filings, including GSTR-1, where the conditions under the relevant rules are satisfied.
- Further scrutiny: Persistent or unexplained mismatches may lead to additional verification, notices, or other action by the GST authorities depending on the facts of the case.
Received a GST Mismatch Intimation?
Kanakkupillai can help reconcile GSTR-1 and GSTR-3B, identify the reason for the mismatch, prepare the required explanation, and assist with GST compliance and notices.
What Is GSTR-9?
GSTR-9 is the annual return under Section 44 of the CGST Act, 2017, read with Rule 80 of the CGST Rules. It consolidates what you reported in your monthly or quarterly returns for one financial year: outward supplies, input tax credit (ITC), tax paid, refunds, demands and HSN-wise summaries. Keeping your regular GST return filing up to date can help you organise the information needed for annual return preparation.
Its real purpose is cross-checking. The department compares it against your GSTR-1, GSTR-3B and GSTR-2B, so any gap between what you declared during the year and what your books actually show tends to surface here. Businesses that identify differences between their sales figures and tax payments should review the process of GSTR-1 and GSTR-3B reconciliation before preparing their annual return.
What Is GSTR-9C?
GSTR-9C is a reconciliation statement under Rule 80(3). It matches the figures in your GSTR-9 against your audited annual financial statements and explains differences in turnover, tax paid and ITC. GSTR-9C is no longer a CA or Cost Accountant certification. For the years when it was an audit-based certificate (FY 2017-18 to FY 2019-20), a professional signed it. From FY 2020-21 onwards, the taxpayer self-certifies the reconciliation statement. Your accounts may still need a statutory audit under the Companies Act or Income Tax Act, but the GST form itself does not require a professional’s certificate.
Who Must File GSTR-9?
Every registered person who was a regular taxpayer during the year must file GSTR-9, unless an exemption applies. The applicable form depends on the taxpayer’s registration category and compliance requirements. Understanding the types of GST returns can help businesses distinguish annual returns from the monthly, quarterly or other returns they may need to file. In practice, the regular taxpayers covered include:
- Proprietorships, partnership firms, LLPs and companies registered as regular taxpayers
- Sellers and service providers whose aggregate turnover is above ₹2 crore
- E-commerce operators and online sellers holding a regular GST registration
- SEZ units and SEZ developers
The return is filed separately for each GSTIN. If you hold registrations in three states under one PAN, you file three annual returns.
Who Does Not Need to File GSTR-9?
| Category | What applies instead |
| Aggregate turnover up to ₹2 crore | Exempt under Notification 15/2025-CT; voluntary filing allowed |
| Composition scheme taxpayers | File GSTR-4 annually. GSTR-9A is no longer in use |
| Input Service Distributors (ISD) | Not required to file GSTR-9 |
| Casual taxable persons | Not required to file GSTR-9 |
| Non-resident taxable persons | Not required to file GSTR-9. See GST registration for foreigners |
| Persons deducting TDS (Section 51) or collecting TCS (Section 52) | Not required to file GSTR-9 for that registration |
How Is Aggregate Turnover Calculated?
The ₹2 crore and ₹5 crore tests use aggregate turnover as defined in Section 2(6) of the CGST Act. It is PAN-based and all-India, so it combines every GST registration you hold under the same PAN. If your business operates across multiple states, it is important to calculate aggregate turnover for GST using the applicable inclusions and exclusions before deciding whether GSTR-9 or GSTR-9C applies. Aggregate turnover includes:
- Taxable supplies and exempt supplies
- Exports of goods and services
- Inter-state supplies
It excludes GST (CGST, SGST, IGST and cess) and inward supplies on which you pay tax under reverse charge. Two practical consequences follow. First, a branch with small sales can still fall inside the ₹5 crore net because the test is applied across the PAN. Second, the figure you compare is turnover for the financial year, not the turnover of a single state.
Who Must File GSTR-9C?
Businesses with an aggregate annual turnover exceeding ₹5 crore are generally required to file GSTR-9C, subject to the applicable GST provisions and exemptions for the relevant financial year. This statement helps reconcile the figures reported in the annual GST return with the corresponding financial records, making it easier to identify differences in turnover, tax liability and Input Tax Credit (ITC).
The turnover threshold is calculated using the PAN-based aggregate turnover across India, rather than the turnover of a single GST registration. However, GSTR-9C is filed separately for each applicable GSTIN. This means that businesses operating in multiple states may need to prepare separate reconciliation statements for their respective GST registrations.
Certain categories of taxpayers, including Input Service Distributors (ISDs), composition taxpayers, casual taxable persons and non-resident taxable persons, are generally excluded from the regular annual return requirements, subject to the applicable rules. Businesses should therefore check their taxpayer category, aggregate turnover and the requirements notified for the relevant financial year before deciding whether GSTR-9C applies to them. Once eligibility is confirmed, checking the applicable GST annual return due date can help businesses plan their reconciliation and filing work in advance.
Do I Need to File? Five Quick Examples
| Situation | GSTR-9 / GSTR-9C |
| Freelance consultant, regular registration, ₹60 lakh turnover | GSTR-9 exempt (optional). No GSTR-9C |
| Private limited company, one state, ₹3.2 crore turnover | GSTR-9 mandatory. No GSTR-9C |
| Trading firm, ₹7 crore across two GSTINs under one PAN | GSTR-9 for each GSTIN. GSTR-9C applies because PAN-level turnover exceeds ₹5 crore |
| Small retailer under composition scheme, ₹90 lakh | GSTR-4, not GSTR-9 |
| Online seller, regular registration, ₹2.5 crore | GSTR-9 mandatory. No GSTR-9C |
Latest GST Updates Affecting GSTR-9 and 9C
These are the changes most likely to affect how you prepare the FY 2025-26 return.
| Update | What it means for you |
| Forms opened for FY 2025-26 (GSTN advisory dated 13 Oct 2026) | GSTR-9 and GSTR-9C for FY 2025-26 were enabled on the GST portal from 8 October 2026. |
| Due date: 31 December 2026 | This is the statutory date under Rule 80. No extension had been notified at the time of writing, so plan for 31 December. |
| ₹2 crore exemption now standing (Notification 15/2025-CT, 17 Sept 2025) | Earlier, the exemption was notified year by year. From FY 2024-25 it applies by a single notification, so small taxpayers no longer wait for an annual announcement. |
| Form changes (Notification 13/2025-CT, 17 Sept 2025) | From FY 2024-25: Table 8A is built on invoices of the year as seen in GSTR-2B; a new Table 8H1 reports IGST on imports claimed in the next year; ITC reversals under Rules 37 and 37A are shown separately; amendments made through GSTR-1A flow into Tables 4 and 5; and GSTR-9C carries a new table for late fee payable and paid. |
| Late fee covers GSTR-9C too (Circular 246/03/2025-GST) | The late fee under Section 47(2) runs until the complete annual return is filed, which includes GSTR-9C where it applies. |
| Two rate regimes in one return (GST 2.0, from 22 Sept 2025) | FY 2025-26 includes supplies at the old 5/12/18/28% rates (April to 21 September 2025) and the new 5%, 18% and 40% structure (from 22 September 2025). Keep both periods clearly separated in your working. |
| Three-year filing bar (Section 44(2), in force from 1 Oct 2023) | An annual return cannot be filed after three years from its due date. The FY 2022-23 return, due 31 Dec 2023, can be filed only until 31 Dec 2026. |
| ITC cut-off (Section 16(4)) | ITC for FY 2025-26 can be claimed up to 30 November 2026 or the date of filing GSTR-9, whichever is earlier. Finish reconciliation before that date, not after. |
Due Date and Late Fee
GSTR-9 and GSTR-9C for FY 2025-26 are due on 31 December 2026. The late fee under Section 47(2) for delay in the annual return, as rationalised by Notification 07/2023-CT for FY 2022-23 onwards, is:
| Aggregate turnover | Late fee per day (CGST + SGST) | Maximum |
| Up to ₹5 crore | ₹50 (₹25 + ₹25) | 0.04% of turnover in the State/UT (0.02% + 0.02%) |
| Above ₹5 crore, up to ₹20 crore | ₹100 (₹50 + ₹50) | 0.04% of turnover in the State/UT (0.02% + 0.02%) |
| Above ₹20 crore | ₹200 (₹100 + ₹100) | 0.5% of turnover in the State/UT (0.25% + 0.25%) |
Taxpayers up to ₹2 crore are exempt, so no late fee arises for them. Interest and any additional tax shown as payable in GSTR-9 or GSTR-9C are separate from the late fee.
Format of GSTR-9 in Brief
GSTR-9 has six parts. You will spend most of your time on Parts II to IV:
- Part I (Tables 1–3): basic details such as GSTIN, legal name and financial year
- Part II (Tables 4–5): outward supplies, taxable and exempt, with amendments from GSTR-1A
- Part III (Tables 6–8): ITC availed, reversed and reconciled with GSTR-2B
- Part IV (Table 9): tax payable and paid
- Part V (Tables 10–14): adjustments declared in the next year’s returns
- Part VI (Tables 15–19): refunds, demands, HSN summaries and late fee
Table 8 is the place where mismatches usually appear, because ITC claimed in GSTR-3B is compared with GSTR-2B. The earlier reference to GSTR-2A on the old version of this page is outdated.
How to Prepare Before You File
- Close all monthly or quarterly returns. Every GSTR-1 and GSTR-3B for the year must be filed first, or the annual return tile will not open.
- Reconcile your sales register with GSTR-1 and GSTR-3B. If you see gaps, read our guide on handling a mismatch between GSTR-1 and GSTR-3B.
- Reconcile ITC with GSTR-2B. Check invoices missing in GSTR-2B and any reversals under Rules 37, 37A, 42 and 43.
- Check HSN and rates. If classification errors surfaced during the year, see how to correct a wrong HSN code in past returns.
- Fix issues in time. Corrections that must go through monthly returns need to be made before the 30 November 2026 cut-off.
- Prepare audited financials if GSTR-9C applies, and note differences in turnover, tax and ITC with reasons.
- Pay any additional liability identified during reconciliation through Form DRC-03 before filing.
A filed GSTR-9 cannot be revised, so review the auto-populated figures and your working carefully before submission.
Common Mistakes to Avoid
- Treating GSTR-9C as a CA certificate and waiting for a professional to “sign off”
- Testing the ₹5 crore limit state by state instead of on PAN-wide turnover
- Filing before the GSTR-1 and GSTR-3B for every month are complete and matched
- Mixing old and new GST rates for supplies on either side of 22 September 2025
- Using GSTR-2A logic for ITC, rather than GSTR-2B
- Assuming a pending annual return can be filed “later”, without checking the three-year bar
- Skipping the return because turnover is below ₹2 crore, without checking whether turnover across all GSTINs under the PAN stays below that limit
What Happens If You Do Not File GSTR-9 and GSTR-9C?
Missing your GST annual return deadline can create more than a compliance headache for your business. Depending on the applicable requirements, delayed filing may result in late fees, notices from the GST department and difficulties in completing your outstanding GST compliance. Continued delays can also affect your ability to file returns if statutory restrictions apply. The consequences depend on the return involved, the relevant financial year and the provisions in force.
The best way to avoid unnecessary complications is to check your filing obligations early, reconcile your books of accounts with your GST returns and address any discrepancies before submitting your annual return. If you have already received a notice from the GST department regarding a pending annual return or a compliance issue, Kanakkupillai can help you understand the notice and prepare an appropriate response. Visit our GST Notice Reply service to explore the support available for your situation.
Why Choose Kanakkupillai for GSTR-9 and GSTR-9C Filing?
Preparing GST annual returns involves more than entering figures into a form. Differences between books of accounts and GST returns, mismatches in Input Tax Credit (ITC), turnover discrepancies and errors in tax reporting can make annual compliance challenging. Identifying these issues before filing helps businesses review their records and address discrepancies appropriately.
Kanakkupillai provides GST compliance and return filing assistance tailored to your business requirements. Our team can help you assess whether GSTR-9 and GSTR-9C apply to your business, review the relevant financial and GST records, identify potential reconciliation issues and understand the information required for filing. We focus on helping businesses maintain consistent records and approach annual GST compliance with greater clarity.
FAQs
Is GSTR-9 mandatory if my turnover is below ₹2 crore?
No. Under Notification 15/2025-CT, a registered person with aggregate turnover up to ₹2 crore is exempt from filing GSTR-9. You may still file voluntarily.
Is GSTR-9C mandatory above ₹5 crore?
Yes. If aggregate turnover exceeds ₹5 crore, you must file GSTR-9C with GSTR-9. It is self-certified, and no CA or CMA certificate is required.
What is the due date for GSTR-9 and 9C for FY 2025-26?
31 December 2026. At the time of writing, no extension has been notified. Always check the GST portal for any later notification.
Can I file GSTR-9 if some GSTR-1 or GSTR-3B returns are pending?
No. The GSTR-9/9C tile on the portal is enabled only after all GSTR-1 and GSTR-3B returns for the year are filed.
Which annual return do composition taxpayers file?
GSTR-4. GSTR-9A is no longer used.
Is turnover of exactly ₹5 crore covered by GSTR-9C?
No. The requirement applies when aggregate turnover exceeds ₹5 crore.
How is aggregate turnover calculated?
It is PAN-based and all-India. It includes taxable, exempt, export and inter-state supplies and excludes GST and reverse-charge inward supplies.
Can I revise GSTR-9 after filing?
No. There is no revision facility, so complete your reconciliation before you submit.
Can I still file the FY 2022-23 annual return?
Only until 31 December 2026, which is three years from its due date under Section 44(2), and only if the related monthly returns are in place.
What is the late fee for GSTR-9?
₹50 a day up to ₹5 crore, ₹100 a day for ₹5 to ₹20 crore, and ₹200 a day above ₹20 crore, subject to the caps in the late fee table above.
