GST Annual Return (GSTR-9) — FY 2025-26 Filing Guide

The GST Annual Return in Form GSTR-9 is a consolidated filing that summarises all monthly or quarterly returns filed during the financial year. It is a mandatory annual compliance requirement for registered taxpayers under the Goods and Services Tax Act, 2017, subject to certain thresholds and exemptions.

This article explains who must file GSTR-9 for FY 2025-26, the GSTR-9C self-certification threshold, the due date, a section-by-section breakdown of the form, common filing errors, and how to avoid them.

Who Must File GSTR-9?

Under Section 44(1) of the CGST Act, 2017 and Rule 80(1) of the CGST Rules, 2017, every registered taxpayer (other than certain exempt categories) must file GSTR-9 for each financial year. The mandatory filing threshold is based on aggregate turnover:

• Aggregate turnover exceeding ₹2 crore: Filing of GSTR-9 is mandatory. This is the standard threshold that applies to most businesses.
• Aggregate turnover up to ₹2 crore: Filing of GSTR-9 is optional. The government has provided this relaxation for small taxpayers through a series of notifications. However, even for optional filings, it is advisable to file GSTR-9 to maintain clean compliance records.
• Aggregate turnover up to ₹5 crore: For GSTR-9C (the reconciliation statement), self-certification is permitted for taxpayers with turnover up to ₹5 crore. This threshold was introduced in 2021 and remains in effect for FY 2025-26.

Note: The ₹2 crore threshold for mandatory GSTR-9 filing is based on the aggregate turnover in a financial year across all states or union territories where the taxpayer is registered. If a taxpayer has multiple GST registrations in different states, the aggregate turnover across all registrations is considered.

Categories Exempt from GSTR-9 Filing

The following categories of registered persons are not required to file GSTR-9:

• Taxed persons under the Composition Scheme (they file Form GST CMP-08 quarterly)
• Non-resident taxable persons
• Taxed persons paying tax under the Reverse Charge Mechanism (RCM) as the sole source of inward supplies
• E-commerce operators required to collect TCS under Section 52 (they file GSTR-8)
• Input Service Distributors (ISD)
• Persons with Unique Identification Number (UIN)

GSTR-9C — Reconciliation Statement

GSTR-9C is a reconciliation statement that must be filed by taxpayers whose aggregate turnover exceeds ₹5 crore during the financial year. It reconciles the turnover declared in the GST returns with the turnover as per the audited financial statements.

Self-Certification Threshold

For FY 2025-26, the following thresholds apply to GSTR-9C:

Aggregate Turnover	GSTR-9C Requirement
Up to ₹5 crore	GSTR-9C is not mandatory. However, if turnover exceeds ₹2 crore, GSTR-9 must still be filed.
₹5 crore to ₹20 crore	GSTR-9C is mandatory. Self-certification by a chartered accountant is permitted.
Above ₹20 crore	GSTR-9C is mandatory. Must be certified by a chartered accountant (not self-certified).

Self-certification: For taxpayers with turnover between ₹5 crore and ₹20 crore, the chartered accountant certifies the reconciliation statement, and the taxpayer self-certifies the GSTR-9C on the GST portal. For taxpayers with turnover above ₹20 crore, the chartered accountant must digitally sign the GSTR-9C on the portal.

Due Date for GSTR-9 and GSTR-9C

For FY 2025-26, the due date for filing GSTR-9 and GSTR-9C is 31 December 2026. This date is prescribed under Rule 80(1) of the CGST Rules. The due date applies to all registered persons required to file these forms, regardless of their filing frequency (monthly or quarterly).

Late fees: Late filing of GSTR-9 attracts a late fee of ₹200 per day (₹100 under CGST and ₹100 under SGST) subject to a maximum of 0.25% of the turnover in the state or union territory. However, the government has from time to time waived or reduced late fees through notifications. Check the latest notification for the applicable late fee for FY 2025-26.

Section-by-Section Guide to GSTR-9

GSTR-9 is divided into multiple parts and tables. Here is a section-by-section breakdown of what data goes where:

Part I — Basic Details (Tables 1-6)

Table	Description	What to Enter
Table 1	Financial Year	Select the financial year (FY 2025-26)
Table 2	GSTIN	Auto-populated from the GST portal
Table 3	Legal name of the registered person	Auto-populated — verify against PAN
Table 4	Trade name (if any)	Auto-populated — the name under which the business operates
Table 5	Whether the taxpayer has multiple GST registrations in the same state	Select Yes or No
Table 6	Whether the taxpayer has opted for the QRMP scheme	Select Yes or No

Part II — Details of Outward and Inward Supplies (Tables 7-12)

Table	Description	Data Source
Table 7	Details of outward supplies (taxable outward supplies)	Auto-populated from GSTR-1 filings. Verify against your books of accounts.
Table 8	Details of outward supplies on which tax is payable under reverse charge	Auto-populated from GSTR-1 filings. Includes supplies where the recipient is liable to pay tax under RCM.
Table 9	Details of inward supplies on which tax is payable under reverse charge	Auto-populated from GSTR-3B filings. Includes inward supplies on which RCM has been paid.
Table 10	Details of exempt supplies	Auto-populated from GSTR-3B (Table 5). Includes nil-rated, exempt, and non-GST supplies.
Table 11	Details of nil-rated supplies	Auto-populated from GSTR-3B (Table 5).
Table 12	Details of non-GST supplies	Auto-populated from GSTR-3B (Table 5). Supplies on which GST is not applicable (e.g., petroleum products, alcohol for human consumption).

Part III — ITC Details (Tables 13-16)

Table	Description	Data Source
Table 13	Total ITC available — as per GSTR-2A/2B	Auto-populated from GSTR-2B (for monthly filers) or GSTR-2B (for quarterly QRMP filers). Cross-check with your purchase register.
Table 14	ITC as per books of accounts	Enter the ITC amount as per your books. This should reconcile with the ITC claimed in GSTR-3B.
Table 15	ITC reversal — ITC available in GSTR-2B but not in books	If GSTR-2B shows ITC that you have not claimed in your books (e.g., because the invoice was reversed or the credit was not eligible), enter the amount here.
Table 16	ITC reversed — ITC in books but not in GSTR-2B	If you have claimed ITC in your books but the invoice does not appear in GSTR-2B (e.g., because the supplier has not filed GSTR-1), enter the amount here.

Part IV — Tax Paid Details (Tables 17-18)

Table	Description	Data Source
Table 17	Details of tax paid as per GSTR-3B	Auto-populated from GSTR-3B filings. Includes CGST, SGST, IGST, and Cess paid through self-assessment.
Table 18	Details of other payments (interest, late fee, penalty)	Enter amounts paid towards interest, late fee, and penalty during the financial year. Cross-check with your payment challans.

Part V — Transactions During the Year (Tables 19-20)

Table	Description	What to Enter
Table 19	Demand and recovery during the year	Details of any demand raised by the department and recovery proceedings during the year.
Table 20	Refunds claimed during the year	Details of GST refund applications filed and the amount refunded during the year.

Part VI — Other Information (Tables 21-22)

Table	Description	What to Enter
Table 21	Supply from SEZ or on which IGST has been paid under Section 7	Details of supplies received from SEZ units or on which IGST has been paid under the IGST Act.
Table 22	HNS-wise summary of outward supplies	HSN code, description, UQC, total quantity, and total value of outward supplies. The HSN summary must be provided if turnover exceeds the prescribed threshold (₹5 crore).

Data Preparation — Before Filing GSTR-9

Before you begin filling in the GSTR-9 form, ensure that the following data preparation steps are completed:

1. Reconcile Monthly/Quarterly Returns

Verify that all GSTR-1 and GSTR-3B returns for the financial year have been filed and the data in those returns is accurate. Any discrepancies between your monthly returns and your books of accounts will surface in the GSTR-9 filing.

2. Reconcile ITC with GSTR-2B

Download the auto-generated GSTR-2B statements for each month and compare them with your purchase register and ITC claimed in GSTR-3B. Ensure that you have claimed ITC only on invoices that appear in GSTR-2B and that you have reversed ITC where required.

3. Reconcile Tax Payments

Match the tax paid in GSTR-3B with the amounts reflected in your Electronic Credit Ledger and Electronic Cash Ledger on the GST portal. Any outstanding tax liability or excess credit should be addressed before filing GSTR-9.

4. Compile HSN-Wise Data

Prepare an HSN-wise summary of outward supplies. For taxpayers with turnover up to ₹5 crore, HSN reporting at the 4-digit level is generally required. For turnover above ₹5 crore, 6-digit HSN codes may be required. Check the latest CBIC notification for the applicable HSN reporting requirements for FY 2025-26.

5. Review Amendments and Corrections

If you have filed any amendments or corrections during the year (through amended GSTR-1 or GSTR-3B filings), ensure that the GSTR-9 data reflects the corrected figures.

Common Errors and How to Avoid Them

1. Mismatch Between GSTR-9 and Monthly Returns

The most common error is a mismatch between the figures reported in GSTR-9 and the figures in the monthly/quarterly returns. This can happen when:

• A return was filed with incorrect data and later corrected, but the correction was not reflected in the annual return
• Data was entered in the wrong table of the monthly return
• An amendment was made in one return but not carried forward to subsequent returns

How to avoid: Before filing GSTR-9, download the auto-populated data from the GST portal and compare it with your books. Use the "Download GSTR-9 JSON" feature to get the pre-filled data and review each table carefully.

2. ITC Reconciliation Failures

ITC claims in GSTR-3B often do not match the ITC available in GSTR-2B. This can result from:

• Suppliers not filing GSTR-1 — their invoices will not appear in your GSTR-2B
• Suppliers filing GSTR-1 with incorrect GSTIN — the invoice will appear under a different GSTIN
• ITC claimed on ineligible invoices — such as ITC on motor vehicles, food and beverages, or personal expenses
• Time limit for claiming ITC — ITC must be claimed within the time limit prescribed under Section 16(4) of the CGST Act

How to avoid: Maintain a purchase register that tracks the GSTIN of each supplier, the invoice date, and the ITC claim status. Reconcile this register with GSTR-2B at the end of each quarter.

3. Incorrect HSN Data

HSN-wise data is often entered with incorrect UQC (unit of quantity), wrong HSN codes, or mismatched quantities. The GST portal validates HSN data against the prescribed format, and errors can cause the return to be rejected.

How to avoid: Use the HSN code search tool on the GST portal to verify HSN codes. Ensure that the UQC matches the unit used in your business (e.g., NOS for numbers, KGS for kilograms, BAG for bags).

4. Not Filing GSTR-9 at All

Some taxpayers with turnover below ₹2 crore assume that GSTR-9 is entirely optional and do not file it. While it is true that filing is optional for turnover up to ₹2 crore, not filing can create issues during assessments or when applying for government contracts, loans, or other business registrations that require GST compliance certificates.

How to avoid: Even if your turnover is below ₹2 crore, consider filing GSTR-9 to maintain a clean compliance record. The form is largely auto-populated, so the filing effort is minimal.

5. Filing GSTR-9 Before All Monthly Returns Are Filed

You cannot file GSTR-9 if any of your monthly or quarterly GSTR-1 or GSTR-3B returns for the financial year are pending. The GST portal will not allow you to submit GSTR-9 until all prior returns are filed.

How to avoid: Before attempting to file GSTR-9, check the "File Returns" dashboard on the GST portal to confirm that all returns for the financial year have been filed. If any returns are pending, file them first.

GSTR-9 Filing Process — Step by Step

1. Login to the GST portal at gst.gov.in using your credentials.
2. Navigate to Services → Returns → Annual Return. Select the financial year (2025-26) and the return filing period.
3. Download the auto-populated data. The portal pre-fills most tables of GSTR-9 based on your monthly/quarterly filings. Download this data and review it against your books.
4. Fill in the remaining tables. Enter any additional data that was not auto-populated, such as HSN-wise details, ITC reconciliation data, and any other information required.
5. Preview the GSTR-9. Use the "Preview GSTR-9" button to generate a PDF of the draft return. Review it carefully before submission.
6. Submit and file. Once you are satisfied with the data, submit the GSTR-9. The return must be filed using a Digital Signature Certificate (DSC) or an Electronic Verification Code (EVC).
7. Download the filed return. After filing, download the acknowledgement and the filed GSTR-9 for your records.

GSTR-9C Filing Process

If your turnover exceeds ₹5 crore and you are required to file GSTR-9C, the process is as follows:

1. Get your accounts audited by a chartered accountant. The audited financial statements must be available before filing GSTR-9C.
2. Prepare the reconciliation statement. Reconcile the turnover as per GST returns with the turnover as per the audited financial statements. Account for any differences — such as exempt supplies, exports, supplies under reverse charge, and inter-branch transfers.
3. Fill in GSTR-9C on the GST portal. The form is divided into two main parts: Part A (reconciliation of turnover) and Part B (reconciliation of tax paid). Fill in the data based on the reconciliation statement.
4. Certification. For taxpayers with turnover between ₹5 crore and ₹20 crore, the chartered accountant certifies the reconciliation statement, and the taxpayer self-certifies on the portal. For turnover above ₹20 crore, the CA digitally signs the GSTR-9C on the portal.
5. Submit and file. Submit the GSTR-9C and pay any additional tax liability arising from the reconciliation.

Practical Considerations for Businesses in Ghaziabad

Businesses in Ghaziabad and across the NCR region should keep the following in mind when preparing for GSTR-9 filing:

1. Start Early

Do not wait until November or December to begin GSTR-9 preparation. Start reconciling your data in August or September. This gives you sufficient time to identify and resolve discrepancies before the 31 December deadline.

2. Multi-State Operations

If your business has GST registrations in multiple states (e.g., separate registrations in Uttar Pradesh, Delhi, and Haryana), you must file a separate GSTR-9 for each registration. Ensure that inter-state supplies between your own registrations are correctly reported.

3. E-Invoice Reconciliation

If your business is required to issue e-invoices (turnover exceeding ₹5 crore), ensure that the e-invoice data is reconciled with your GSTR-1 filings. The e-invoice system generates IRN (Invoice Reference Number) for each invoice, and this data flows into your GSTR-1 automatically.

4. E-Way Bill Data

If your business generates e-way bills for goods movement, the e-way bill data should be reconciled with your outward supply details. Discrepancies between e-way bills generated and invoices reported in GSTR-1 can attract departmental queries.

5. Seek Professional Assistance

GSTR-9 filing involves reconciling data from multiple sources — GSTR-1, GSTR-3B, GSTR-2B, books of accounts, and financial statements. For businesses with complex operations, multiple registrations, or significant ITC discrepancies, it is advisable to engage a chartered accountant to handle the filing and reconciliation.

Summary

Key Point	Details
Mandatory filing threshold (GSTR-9)	Aggregate turnover exceeding ₹2 crore
Optional filing threshold (GSTR-9)	Aggregate turnover up to ₹2 crore
GSTR-9C threshold	Aggregate turnover exceeding ₹5 crore (self-certification up to ₹20 crore)
Due date	31 December 2026 (for FY 2025-26)
Late fee	₹200 per day (₹100 CGST + ₹100 SGST), max 0.25% of turnover per state
Filing mode	GST portal — DSC or EVC required for submission
Key data sources	GSTR-1, GSTR-3B, GSTR-2B, books of accounts, audited financial statements
HSN reporting	4-digit (turnover up to ₹5 crore) or 6-digit (turnover above ₹5 crore)

Filing GSTR-9 is a consolidation exercise that brings together all the data from your monthly or quarterly GST filings. By starting early, reconciling data carefully, and addressing discrepancies before filing, you can complete the annual return accurately and within the deadline.

For assistance with GSTR-9, GSTR-9C, or any other GST compliance matter in Ghaziabad or across the NCR, you can reach out at +91 8802586988 or visit caashishrajput.com.