Mastering GSTR 9C: Applicability, Reconciliation and Filling

GSTR 9C is an annual reconciliation statement filed by Goods and Services Tax (GST). This is for businesses whose annual turnover exceeds a specified limit. It aligns the data reported in GST returns with the audited books of accounts of the company. This blog will explain to you in detail what GSTR 9C is, who must file it, the turnover limit, due dates, detailed format, the new changes, and why it matters. Read to know more.

Before proceeding with why GSTR 9C is important and the filling process, here first we will discuss about what is GSTR 9C. 

What is GSTR 9C?

GSTR 9C is a self-certified reconciliation statement. Read the section below to know what it comprises of: 

1. Figures reported in GSTR-9(the annual GST return), and
2. Figures recorded in the taxpayer’s audited financial statements for the same financial year.

What is its Purpose?

Here we will have a discussion about the purpose of GSTR 9C. 

Its purpose is verifying the consistency between the GST data submitted throughout the year and what is recorded in the company’s books. However, explanation is needed for any mismatch with valid reasons, and if a tax difference exists, the taxpayer must pay the additional liability through Form DRC-03. An entity with multiple GST registrations across states must file separate GSTR-9C statements for each registration, as this form is filed per GSTIN.

Why is GSTR-9C Important?

GSTR 9C acts is a checkpoint for both businesses and tax authorities. Therefore, the importance of GSTR 9C is summarized as below:

• Ensures accuracy: It mainly validates the correctness of turnover, input tax credit (ITC), tax payments, and liabilities that are declared during the year. Therefore, it helps in ensuring accuracy.
• Reduces departmental queries: Transparent reconciliation will lead to fewer GST notices and audits. Thus it helps in reducing departmental queries
• Strengthens audit trail: It helps in creating a strong financial trail and improves compliance hygiene. Therefore, it strengthens the audit trail. 
• Helps businesses self-identify gaps: Businesses can proactively correct errors, mismatches, or missed liabilities. Thus it helps businesses in self-identifying their gaps. 
• Mandatory for large taxpayers: Compliance risk is extremely important for businesses who have a 5 crore turnover, making GSTR9C an important regulatory requirement. Therefore, it is vital for large taxpayers. 

Hope this section has made it clear to you why GSTR 9C is important. 

GSTR 9C Applicability & Turnover Limit

Here we will have an in-depth discussion on GSTR 9C Applicability and Turnover Limit. 

Filing GSTR 9C is mandatory as per CBIC Notification No. 30/2021 dated 30 July 2021. Read the section below to know the applicability for GSTR 9C. 

The Annual aggregate turnover of the business is exceeding Rs. 5 crores in a financial year. In that case it is mandatory.

If the turnover of the business is Rs 5 crore or below, filing GSTR-9C is not required. In that case you can skip filling for GSTR 9C.

Exemptions

However, there are certain categories of taxpayers who are exempt from filing GSTR 9C. Read the section below to know who are not need to file it. 

• Foreign airlines operating in India are exempt under Notification No. 09/2020 (16 March 2020), provided they will have to comply with prescribed rules under the Companies Act.
• Non-resident OIDAR service providers supplying to unregistered persons are exempt under Notification No. 30/2019 (28 June 2019).

These exemptions help in reducing the compliance burden for foreign entities and providers who offer specialized cross-border services.

Due Date for Filing GSTR-9C

An individual will have to file GSTR 9C on or before 31 December of the year thus following the relevant financial year.

Example

For instance FY 2024–25, the due date is:
 31 December 2025

However, the government can extend the deadline if required. In case if you fail to file within the deadline then you will have to pay late fees and penalties. We have discussed those in one of the upcoming sections of the blog.  Read to know. 

GSTR 9C Format: Two Major Components

Therefore, in this section we will have an in-depth discussion on what GSTR 9C comprises of: 

Part A – Reconciliation Statement

This is the main portion of GSTR 9C and is divided into five sections. Therefore, read the section to know details about the 5 vital parts that the reconciliation statement consists of:

• Part I – Basic Details

It includes general identification details such as GSTIN, legal name, and trade name. Therefore, part I of the reconciliation statement consists of basic details.

• Part II – Reconciliation of Turnover

Therefore, in comparison to turnovers that are reported in the audited financial statements with turnover disclosed in GSTR 9, 

This section includes adjustments for:

• Unbilled revenue
• Advances
• Credit notes
• Supplies not part of GST turnover
• Exempt or non-GST supplies
• Part III – Reconciliation of Tax Paid

Thus, make sure that tax paid in GSTR-9 is matching with tax payable based on books after adjustments.

• Part IV – Reconciliation of Input Tax Credit (ITC)

ITC as per books is matching with ITC declared in GSTR 9. However, any mismatch will be categorized into eligible, ineligible, and reversed ITC.

• Part V – Additional Liability

Any unreconciled differences that result in additional tax need to be reported here, and payment should be made through Form DRC-03.

Part B – Self-Certification

Here we will have discussion on Part B i.e the Self-Certification for GSTR 9C.

Previously certification by a CA or CMA was required for GSTR 9C. However now taxpayers can themselves certify the statement.

The self-declaration basically confirms that the reconciliation has been performed and all discrepancies have been disclosed truthfully.

Recent Changes Made to GSTR 9C (Effective FY 2024–25)

Multiple updates are introduced for enhance transparency and strengthen compliance. Here we are providing a simplified breakdown. Check it out:

1. Mandatory Tables 12B & 12C – Cross-Year ITC Reporting

Taxpayers will have to disclose ITC pertaining for the year 2024–25 reversed for the year 2025–26 and ITC for the year 2024–25 availed for the year 2025–26.

This will ensure that ITC can be traced beyond the year of origin from availing to reversal.

2.No More Catch-All Table 5O – Separate Turnover Adjustments

Previously there were various adjustments under Table 5O. However presently, adjustments are report individually in specific tables (5B, 5C, 5D, etc.), such as Unbilled revenue, Advances and Supplies treated differently in books vs GST returns. This improves the clarity and reduces ambiguity at the time of audit.

3. Introduction of Table 7D1 – Supplies via E-Commerce Operators (ECO)

For reporting transactions, a new requirement is there where tax is paid by the e-commerce operator under Section 9(5). This will help in aligning taxpayer and ECO data. It will help in avoiding mismatch notices.

4. Auto-Calculated Late Fee – Table 17 (New)

GSTR-9C will now display automatic late fee computation:

• 100 per day for GSTR-9, and
• 100 per day for GSTR 9C

Taxpayers need to pay this through DRC-03.
Automation will reduce errors and increases timely filing.

5. Mandatory Expense-Wise ITC Reporting – Table 14

Expense categories such as:

• Rent
• Repairs & maintenance
• Legal fees
• Capital goods
• Other service expenses

All these require detailed ITC breakdown. This will help authorities verifying ITC accuracy and detect ineligible claims.

Why Do These Changes Matter?

These updates aim to:

• Helps in improving reconciliation quality
• Offer better transparency into taxpayer operations
• Will help in strengthening ITC monitoring
• Helps in enhancing compliance accuracy
• Reducing the number of audit objections

Thus the revised structure is moving towards data-driven GST oversight.

How to File GSTR 9C?

Given below the steps for filing GSTR 9C: 

1. Prepare audited annual accounts
2. Ensure completion of GSTR 9on the GST portal
3. Download GSTR 9C offline utility in case if you are using offline method
4. Reconcile turnover, ITC, tax, and adjustments
5. Provide reasons for mismatches
6. Compute additional tax liability if there are any
7. Pay additional liability via DRC-03
8. Upload JSON file if you are filling offline
9. Submit & self-certify the form

Penalty & Late Fee for GSTR-9C

According to the current rules we have provided the late fees and penalties below:

• Late fee is 100 per day for CGST including Rs. 100 per day for SGST
• Maximum limit is 0.25% of turnover in the State/UT for CGST + 0.25% for SGST (total 0.5%) This is equal to 0.5% of turnover.

Note: Delayed filing will increase the risk of scrutiny and departmental audits.

Conclusion

GSTR 9C plays helps in establishing transparency between the financial statements of a business and its GST filings.  Taxpayers who have a turnover exceeding Rs. 5 crores should consider GSTR-9C preparation as an extremely important step for maintaining financial hygiene of a company rather than a mere compliance requirement. Proper reconciliation will reduce risks, enhance credibility, and ensures smooth GST operations across reporting years. If you have any query, get in touch with Online Legal India.

Frequently Asked Questions

1. Is GSTR-9C still applicable?

Yes. It is mandatory for taxpayers who have a turnover above Rs. 5 crores.

2. Is it mandatory to get GSTR 9C certified by a CA?

No. Presently it is not required. The requirement is replaced with self-certification by the taxpayer.

3. Can I claim ITC in GSTR 9C?

No new ITC can be claimed in GSTR-9C. If excess ITC was availed, the taxpayers will have to reverse it. If ITC was missed earlier, then in that case it must be claimed in regular GST returns within allowed timelines.

4. What turnover is considered for GSTR 9C applicability?

Aggregate turnover (PAN level) including:

• Taxable supplies
• Exempt supplies
• Exports
• Inter-state supplies

5. How do I download an error report for GSTR 9C?

The error report will be available in the GSTR-9C dashboard under the "Offline Upload" section on the GST portal.

6. Which tables are compulsory?

All reconciliation tables, mandatory ITC tables, and verification sections need to be completed. System-generated tables (like Late Fee Table 17) will get auto-populated.

Disclaimer:

This article is for informational purposes only and does not constitute legal advice. Online Legal India is a digital platform. If you require legal assistance, we strongly recommend consulting a qualified lawyer or law firm.