How to File GSTR-9 and GSTR-9C: A Step-by-Step Annual GST Compliance Guide

  • 23 Oct 2025
  • GST
  • Comments Off on How to File GSTR-9 and GSTR-9C: A Step-by-Step Annual GST Compliance Guide
GSTR-9

How to File GSTR-9 and GSTR-9C: A Step-by-Step Annual GST Compliance Guide

GSTR-9

As the financial year 2024–25 draws to a close, one of the most important GST compliance tasks approaches — filing GSTR-9 (Annual Return) and GSTR-9C (Reconciliation Statement).

The GST portal went live for annual return filing on October 14, 2025, and the due date for both forms is December 31, 2025, unless extended. This guide breaks down everything you need to know — from eligibility and latest notifications to a step-by-step filing walkthrough.

1. Understanding GSTR-9 and GSTR-9C

GSTR-9: Your Annual GST Report Card

GSTR-9 consolidates the entire year’s GST data — outward and inward supplies, tax paid, and input tax credit (ITC) availed — based on your monthly or quarterly GSTR-1, GSTR-3B, and GSTR-2B filings.

Think of it as your “year-end GST scorecard”, summarizing your compliance performance for the fiscal year.

GSTR-9C: The Reconciliation Bridge

GSTR-9C reconciles figures between your audited financial statements and the details reported in GSTR-9.
It identifies gaps, such as differences in turnover, tax paid, or ITC claimed.

Since FY 2020–21, GSTR-9C has been self-certified — no longer requiring a Chartered Accountant’s attestation (per the amendment to Section 35(5) of the CGST Act).

⚠️ Late Filing Warning: Delays attract late fees under Section 47(2) of the CGST Act. However, several recent relaxations have reduced penalties for previous years.

GSTR-9

2. Applicability and Turnover Thresholds

FormWho Needs to FileTurnover ThresholdKey Notes
GSTR-9Regular taxpayers filing GSTR-1 & 3B> ₹2 croreExempt for ≤ ₹2 crore (permanent exemption from FY 2017–18)
GSTR-9CTaxpayers also required to file GSTR-9> ₹5 croreSelf-certified reconciliation; exemptions continue for foreign airlines (Notification 09/2020) and OIDAR non-residents (Notification 30/2019)

👉 Important Tip:
Turnover is calculated at the PAN level (aggregate pan-India turnover), but filing happens per GSTIN. Businesses operating in multiple states should reconcile figures across registrations well in advance.

3. Key Notifications and Circulars for FY 2024–25

The GST Council and CBIC have released several important updates impacting FY 2024–25 filings:

🔹 Notification No. 13/2025–CT (September 22, 2025)

  • Revised formats of GSTR-9 and GSTR-9C

  • New ITC splits for current vs. previous financial years (Tables 6A1 & 6A2)

  • Disclosure of ITC reversals (Rules 37, 42, etc.)

  • Tracking deferred ITC and e-commerce supplies under Section 9(5)

  • Enhanced reconciliation in Table 9 for cash vs. ITC-ledger payments

🔹 Notification No. 15/2025–CT (September 17, 2025)

Continues GSTR-9 exemption for taxpayers up to ₹2 crore turnover (extension of FY 2023–24 relief under Notification 14/2024).

🔹 Circular No. 246/03/2025–GST (January 30, 2025)

  • Clarifies late fee applicability for delayed GSTR-9C when GSTR-9 is timely filed.

  • Late fee applies until both returns are submitted.

🔹 Notification No. 08/2025–CT (January 23, 2025)

  • Waiver of excess late fees for FY 2017–18 to 2022–23 if GSTR-9C filed by March 31, 2025 (no refund for already paid amounts).

🔹 55th GST Council Update (Upcoming)

  • Expected waiver of late fees for earlier-year GSTR-9C filings beyond GSTR-9 submission date.

  • Introduction of a new turnover-based late fee cap (effective FY 2022–23 onwards):

Turnover RangeDaily Fee (CGST+SGST)Max Fee (% of Turnover)
≤ ₹5 crore₹500.04%
₹5–20 crore₹1000.04%
> ₹20 crore₹2000.50%

4. Step-by-Step Guide: Filing GSTR-9

GSTR-9 is mostly auto-populated, but discrepancies can arise. Here’s a simple workflow:

Step 1: Prepare Your Data (1–2 Weeks Before Filing)

  • Ensure all GSTR-1, 3B, and 2B are filed for FY 2024–25

  • Download GSTR-2A/2B summaries from the GST portal

  • Reconcile:

    • Outward supplies (GSTR-1 vs. GSTR-3B)

    • ITC (GSTR-2B vs. purchase ledger)

Step 2: Reconciliation & Review

  • Identify ITC reversals under Rule 42/43 for exempt supplies.

  • Separate ITC into:

    • Current year claims

    • Previous year claims (deferred)

  • Tally import IGST with ICEGATE data.

Step 3: Fill Out GSTR-9 (Tables 1–19)

On the GST portal:

  • Go to Returns → Annual Return → GSTR-9

  • Auto-fill using JSON data from your accounting software

  • Sections Overview:

    • Part I (Tables 1–5): Basic info, outward supplies

    • Part II (Tables 6–8): Inward supplies & ITC (with new ITC splits)

    • Part III (Tables 9–11): Tax paid, HSN details

    • Part IV (Tables 12–18): Amendments, refunds, debit/credit notes

    • Part V (Table 19): Late fee details

Step 4: Settle Any Additional Liability

If underpaid tax is detected, pay via Form DRC-03, selecting “Reconciliation Statement”.

Step 5: Upload & File

  • Verify via DSC or EVC

  • Submit and download the ARN (acknowledgment reference number)

🚫 No revision option — double-check before submission.

5. Step-by-Step Guide: Filing GSTR-9C

For taxpayers with turnover > ₹5 crore, GSTR-9C ensures books align with GSTR-9.

Step 1: Gather Data

  • Obtain audited financial statements (PAN-level)

  • Reconcile across all GSTINs

  • Tag e-commerce data per Notification 13/2025

Step 2: Prepare Part A – Reconciliation

  • Part I: Basic details

  • Part II (Tables 5–6): Reconcile turnover (gross vs. GSTR-9)

  • Part III (Tables 7–11): Reconcile tax paid, rate-wise differences

  • Part IV (Tables 12–14): Reconcile ITC (eligible vs. ineligible)

Step 3: Self-Certify & File

  • No CA certification needed

  • Pay additional liability (if any) via cash or ITC

  • Upload along with GSTR-9

✅ Once both forms are filed, the return is marked as “Complete” per Circular 246/2025.

7. Expert Tips for Smooth Filing

💡 Go Digital: Use GSTN’s offline utility or ERP integrations (Tally, Zoho, SAP).
💡 Reconcile Early: Don’t wait till December — avoid auto-lock errors.
💡 Track ITC Journey: Distinguish between claimed, deferred, and reversed ITC.
💡 Avoid Misses: GSTR-9C is mandatory for >₹5 crore turnover — GSTR-9 alone is incomplete.
💡 Plan Ahead: The amnesty scheme for old years ends March 2025 — act now!

❗Non-filing attracts a general penalty of up to ₹25,000 under the CGST Act.

Read More: Salary Income Taxation: Key Provisions of the Income Tax Act 2025

Conclusion

Filing GSTR-9 and GSTR-9C isn’t just about compliance — it’s a yearly opportunity to reconcile your business’s financial truth with GST records. With the 2025 changes emphasizing ITC transparency and turnover-based fee limits, timely filing ensures a clean GST slate and stronger financial credibility.

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GST Intermediary Dispute Remains Unresolved

GST Intermediary Dispute Remains Unresolved

Recently, a circular -159/51/2021-GST-Clarification on Doubts Regarding the Scope of ‘Intermediary’ was released, but I’m not sure if the doubts were cleared or persisted…

First and foremost, the term “intermediary” is defined as “a person who acts as a middleman between two parties.”

‘A broker, an agent, or any other person, by whatever name called, who arranges or facilitates the supply of goods or services, or both, or securities, between two or more persons, but does not include a person who supplies such goods or services, or both, or securities on his own account,’ says the definition.

The term “intermediary” was borrowed from the Service Tax Regime in the GST. As stated in the circular, the scope of ‘’intermediary services” under the GST REGIME does not differ from the scope of ‘’intermediary services” in the Service Tax REGIME.

The circular merely mentions who is a middleman, however, it is unclear if the services provided by the intermediary are considered exports of services or not –– the debate continues —–

Read More…

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Several instances are offered in a circular format but are only described once

Who is the intermediate

I.e., who arranges or facilitates the provision of products or services, i.e., a third party between two parties, although it is unclear if intermediary services are exportable or not?

Let’s look at an example:

A- Machine Manufacturer and Supplier in India

B- if you want to buy a machine but don’t live in India.

C- Assists ‘’B” in identifying customers –

C acts as an intermediary, invoicing ‘’B” in order to complete the transaction between ‘’A” and ‘’B”.

Non-filers of monthly GST returns would be prevented from filing GSTR-1 from next year. 

Why can’t C’s services be classified as exports of services because he provides services outside of India?

The supply of any service when it is exported is referred to as service export.

  • Supplier of service located in India –i.e A and C
  • Recipient of service located outside India- i.e B
  • Payment for such service received in convertible foreign exchange.
  • Place of supply of service is outside India – as per Sec 13(8) clause (b) IGST ACT 2017

IN THE CASE OF INTERMEDIARY SERVICE – SUPPLY PLACE – SUPPLIER LOCATION

The location of the supplier in India does not justify the export of services in this case.

The foregoing is still disputed, and litigation is ongoing, according to the circular.

Conclusion: If GST is a destination-based consumption tax, and C is providing a service to B – OUTSIDE INDIA, and payment is made in convertible foreign currency, why can’t it be classified as a service export?

So, unless the government clarifies the above, the litigation will continue.

Non-filers of monthly GST returns would be prevented from filing GSTR-1 from next year.

Non-filers of monthly GST returns would be prevented from filing GSTR-1 from next year.

Businesses that fail to file a summary return or pay monthly GST will be unable to file a GSTR-1 sales return for the following month beginning January 1 of the following year. The GST Council met in Lucknow on September 17 and resolved on a slew of steps to simplify compliance, including requiring firms to use Aadhaar authentication when filing refund claims.

These steps will aid in preventing revenue leakage from the Goods and Services Tax (GST), which was implemented on July 1, 2017.

With effect from January 1, 2022, the Council agreed to alter Rule 59(6) of the Central GST Rules to specify that a registered person will not be allowed to file Form GSTR-1 if he has not filed the previous month’s return in Form GSTR-3B.

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Currently, the legislation prohibits businesses from filing a report for outward supplies, or GSTR-1, if they have not filed a GSTR-3B for the previous two months.

Businesses file GSTR-1 for a given month by the 11th day of the following month, but GSTR-3B, which is used to pay taxes, is filed in a staggered fashion between the 20th and the 24th day of the following month.

The GST Council has also made the Aadhaar authentication of GST registration essential for filing refund claims and applications for registration revocation or cancellation.

New GST registration denial have a serious impact on our economy 

With effect from August 21, 2020, the Central Board of Indirect Taxes and Customs (CBIC) has notified Aadhaar authentication for GST registration.

The announcement also stated that if a business does not give an Aadhaar number, GST registration will only be approved after a physical inspection of the business location.

Businesses will now be required to link their GST registration with biometric Aadhaar in order to claim tax refunds and apply for revocation or cancellation of registration, according to the Council.

In its 45th meeting, the Council, which consists of central and state finance ministers, also determined that GST refunds will be paid into the same bank account as the PAN used to get GST registration.