GSTR-9/9C FY 2024-25: Mandatory Changes and Reconciliations

Introduction

It has been 8 years since GST has been implemented. Since then, many changes were seen by way of notifications, circulars & advance rulings. The annual return is one of the major aspects of GST law.

The basic understanding of the adjustments, reconciliations that are to be performed while filing an annual return and reconciliation statement (GSTR 9 & GSTR 9C resp.) and along with required reconciliations, best practices, advanced issues & solutions and tips as applicable for financial year (FY) 2024-25 are covered in this article.

Govt. changes w.r.t GSTR 9 & 9C FY 24-25:

• NN 13/2025-CT dated 17th September 2025
• Updated Form GSTR 9 & GSTR 9C available in CBIC portal (GST > Forms > Returns)
• FAQ on GSTR 9/9C for the FY 2024-25 by GSTN.

What are the different forms of annual return?

There are 3 different forms of annual returns under the GST law. They are:

• GSTR 9 – to be filed by regular registered taxpayers who file GSTR 1 and GSTR 3B.
• GSTR 9A – to be filed by registered composite dealers (composition scheme).
• GSTR 9B – to be filed by e-commerce operators who collect tax at source and have filed GSTR 8 during the financial year (Not yet notified for filling).

What is GSTR 9?

As per section 44 of CGST Act read with Rule 80(1) of CGST Rules, GSTR 9 is an annual return to be filed by every registered taxpayer other than CTP, ISD, NRTP, and TCS & TDS deductors. The return consists of details such as outward/inward supplies, taxes paid, refund claimed and demands raised.

What is GSTR 9C?

GSTR 9C is a reconciliation statement, which is to be filed annually by taxpayers. However, registered persons whose aggregate turnover Rs. 5 crores or more

It is a reconciliation statement between the filed annual return and the audited annual financial statement of the taxpayer.

As per section 2(6) of the CGST Act, “aggregate turnover” means the aggregate value of all taxable supplies (excluding the value of inward supplies on which tax is payable by a person on a reverse charge basis), exempt supplies, exports of goods or services or both and inter-State supplies of persons having the same Permanent Account Number, to be computed on all India basis but excludes central tax, State tax, Union territory tax, integrated tax, and cess.

Who should ϐile an annual return?

As per section 44 of the CGST Act, all taxpayers/taxable persons registered under GST must ϐile their annual return i.e., each GSTIN will have to ϐile a separate annual return in case of multiple registrations under a single PAN. However, the following categories are NOT required to ϐile an annual return:

• Casual Taxable Person
• Input service distributors
• Non-resident taxable persons
• Persons paying tax under section 51 (TDS) or 52 (TCS) of the CGST Act.

Proviso: Any department of the CG or an SG or a local authority, whose BOAs are subject to audit by the C&AG, or an auditor appointed for auditing the accounts of local authorities under any law.

Provided that the Government, by notiϐication, may exempt any class of registered persons from ϐiling an annual return.

Changes are notiϔied in the form GSTR-9 for FY 2024-25 vide CGST notification 16/2025 dated 17th September 2025. Registered persons with aggregate turnover up to Rs.2 crore are exempt from ϔiling the annual return for FY 2024-25 onwards vide CGST notiϔication 15/2025.

What is the due date for ϐiling an annual return?

The due date for ϐiling an annual return is the 31st of December of the following year. For example, the due date of GSTR-9 for FY 2024-25 will be 31st December 2025. GSTR 9C i.e., reconciliation statement is considered as a part of the ‘annual return’.

What is the late fee for delay in ϐiling annual return?

As per section 47(2) of the CGST Act, the late fees for not ϐiling the annual return within the due date is Rs 100 per day, per Act. Thus, the total liability is Rs 200 per day by default to a maximum limit of 0.50% of the taxpayer’s turnover (GSTIN turnover). However, the delay in ϐiling GSTR 9C may attract a

general penalty u/s 125 of CGST Act, which may extend up to ϐifty thousand rupees (CGST+SGST).

This view is disputable as the GSTR 9C can be considered to be a part of ‘annual return’ and therefore, where mandatory, late fees may apply on delayed ϔiling of GSTR 9C too.

Key reconciliations required to be performed under GST Audit

The reconciliations ensure accuracy of turnover, tax liability, ITC, and closing balances across Books, GST returns, and AFS, identifying any mismatches, timing differences, or compliance gaps.

1. Turnover – AFS vs GSTR-9C (Table 5A)

• Ensure consolidated turnover (all GSTINs) in AFS matches with Table 5A of GSTR 9C.

2. AFS vs GSTR-9 (Turnover Reconciliation)

• Major reconciliation for Table 5 of GSTR 9C.
• Identify differences between turnover in AFS and GSTR-9.
• Adjustments include unbilled revenue, advances, deemed supplies, export incentives, interest, subsidies, etc.

3. Taxable Turnover – AFS vs GSTR-9 (Table 7 of GSTR 9C)

• Derive taxable turnover after reducing exempt, nil-rated, non-GST, zero-rated (without tax), and RCM supplies from total turnover.

4. Outward Tax Liability – Books vs GSTR 3B + DRC-03

• Tax liability shown in books must match with tax actually paid through returns.
• Excess paid → adjust next year.
• Short paid → pay via DRC-03.

5. Adjustments & Additional Liabilities

• Consider subsequent year adjustments, audit findings, interest and delay payments for variance reasons.

6. Rate-wise Outward Tax Liability

• Match rate-wise liability as per workings vs books.
• Differences may arise from wrong rate application or accounting errors.

7. GSTR-1 vs GSTR-3B

• Perform reconciliation:
  • √ If equal → no issue.
  • ×If mismatch → do invoice-level reconciliation.
    • GSTR 1 > 3B → additional tax liability; pay via DRC-03.
    • GSTR 1 < 3B → excess tax paid; adjust/refund next year.
• Reflect subsequent adjustments in Part V of GSTR-9.

8. Inward Taxes (ITC) – Books vs GSTR-3B

• ITC in books (eligible o nly) should equal ITC in GSTR-3B.
• Excess claimed → reverse via DRC-03.
• Short claimed → avail in next 3B (within time limit u/s 16(4)); else expense.

[Map invoice level ITC register with Net ITC availed in 3B (Ensure 3B invoice level includes clear description, HSN code, GL code etc. and tag relevant GL’s, product description, Tax details etc.]

9. GSTR 2B vs Books

• ITC in 2B (eligible) should match with books.
• √ Equal → no issue.
• Books > 2B → vendor non-reporting, timing, or prior-year ITC.
• Books < 2B → ineligible ITC, wrong GSTIN by supplier, or missed claims.

10. Closing Balances – Books vs GST Portal

• Reconcile cash + credit balances in books with e-ledgers on portal (all GSTINs).
• If mismatch → do invoice-level reconciliation.
• Handle short/excess ITC, pre-deposits, or under-protest ITC

11. Spillover Transactions

• Transactions of one FY reported in next FY’s returns.
• Include invoices, credit/debit notes, advances, ITC claims/reversals.
• Reflect in Part V of GSTR-9 for current FY and Part II of next year.

12. Imports – ICEGATE vs Books vs GSTR-3B

• Match import data in ICEGATE, Books, and GSTR-3B.
• Ensure ITC (IGST/Cess) claimed equals actual BOE values.
• Note: No time limit for claiming ITC on import of goods (Section 16(4) applies only to invoices/debit notes).

13. Reconcile 3B invoice level ITC register vs E-invoicing data

14. Reconcile Invoice level ITC register with Expenses GL & relevant B/sheet GL’s

15. Reconcile E-way bill data to Sales register

Form GSTR 9 – Annual Returns

I. Key Changes in ITC Reporting

1. Table 6 – ITC Segregation:

• ITC pertaining to previous year and current year to be distinctly reported under Table 6A(1) and 6A(2).

2. Table 6H – Reclaimed ITC:

• First-time claim to be reported in Table 6B.
• Reversal to be disclosed in Table 7, and subsequent reclaim in Table 6H.
• ITC reversed earlier under Rule 37 or 37A (up to FY 2023-24) and reclaimed in FY 2024-25 to be shown in Table 6H.
• Any other ITC reversed in prior years but claimed in current year to be shown in Table 6A(1).

3. Table 6M – ITC-02 Reporting:

• Separate disclosure required for ITC-02.
• Revised wording—this table can no longer be used as a general/residuary ITC category.

4. Table 7A1 & 7A2 – ITC Reversals:

• Rule 37 (non-payment to vendor within 180 days).
• Rule 37A (vendor’s GSTR-3B filing status).

II. Disclosures added in annual returns format.

1. Table 7 – All ITC reversals to be disclosed separately. Cannot be consolidated under Table 7H from FY 24-25 onwards.

2. Table 8A will be based on table 6B only from FY 2024-25 onwards. ITC reclaimed will not be reported in Table 8B, delinked from table 6H. Also, this table depicts ITC as per table 3(I) of Form GSTR 2B (from FY 23-24).

3. Table 8H1 introduced – ‘IGST Credit availed on Import of goods in next ϐinancial year’ to help bifurcate ITC reconciliation on import of goods in table 8.

4. Table 6J & table 8I – Difference calculations are modiϐied to keep the effect of above changes. Table 6J is suggested to be maintained as zero.

5. Table 9 will now have upfront reporting of the difference between tax payable and tax paid. To ensure clear reasons for positive variance and payment proof for negative variance.

6. Tables 10, 11, 12, and 13 have undergone cosmetic changes, i.e. ‘Particulars of the transactions for the ϐinancial year declared in returns of the next ϐinancial year till the speciϐied period’.

7. Table 12 & 13 are now mandatory – ITC of FY 24-25, claimed and reversed in GSTR 3B of FY 25-26 (before 30th Nov.)

8. Payment of additional tax liability – Form GSTR 9 earlier mentioned to be paid in cash, now allows utilisation of input tax credit. Although, GST portal allowed credit utilisation in line with GST law.

III. The relaxations that remain from the past are as follows:

9. Table 4 – Amendments, credit notes and debit notes cannot be shown as net ϐigures in B2B, B2C, etc. now. Table 4I to 4L to be disclosed separately from FY 21-22

10. Table 5 – Exempted & Nil-rated can be consolidated in ‘Exempted’ column or shown separately. Table 5F – Non-GST to be shown separately from FY 21-22 onwards

11. Table 17 – HSN outward details mandated from FY 2021-22 onwards. (GSTR 1 (table 12) consolidated data can be used for table 17).

12. HSN disclosures to be performed at 6-digit level (when T/o > Rs. 5 crore) and 4-digit level (when T/o < Rs. 5 crore for B2B only)

13. Clariϐication that disclosures in GSTR 1 tables 9A, 9B & 9C must be disclosed in table 10 & 11 of GSTR 9.

14. Table 5 – Amendments, credit notes and debit notes can be shown as net ϐigures in table 5.

15. Table 6 – ITC bifurcation into ‘inputs’/’input services’ not mandatory, total value can be consolidated under ‘Inputs’. From FY 2019-20 – under ‘Inputs’ & ‘Capital Goods’.

16. Table 6 – May consolidate ITC under RCM from registered and un-registered persons under registered persons’ table.

17. Part V – Reversal/Availment of ITC in previous year may not be ϐilled (T12 & T13)

18. Table 15, 16 & 18 – Refund details, Info on inward supplies & deemed supply, HSN inward details remain optional.

IV. Clarification on Outward Supply disclosures:

19. Table 4G1 & 5C1 – E-commerce operator supplies liable under section 9(5) –Source of info – GSTR 1 – table 14(b), 15 & table 3.1.1.ii & i – GSTR 3B [ECO & Supplier respectively].

20. Consider return ϐiling w.r.t GSTR 1A where applicable (along with GSTR 1).

21. HSN Table 17 – advances and schedule III items must not be disclosed here.

22. Outward supply of FY 23-24 disclosed in GSTR 3B of FY 24-25, where shown in GSTR 9 FY 23-24 in table 10 or table 11 – Should not form part of table 4 or 5 of GSTR 9 FY 24-25. [short/excess taxes paid in 23-24 adj. in 24-25]

• Reason – already disclosed and reconciled in GSTR 9 & 9C of FY 23-24
• Impact – Table 9 of GSTR 9 FY 24-25 would show this positive variance (not compensatory in nature)

23. Credit Note raised in FY 23-24 disclosed in GST returns of FY 24-25, where shown in GSTR 9 table 4 of FY 23-24 – Should not form part of table 4 or 5 of GSTR 9 FY 24-25.

• Reason – already disclosed and reconciled in GSTR 9 & 9C of FY 23-24
• Impact – Table 9 of GSTR 9 FY 23-24 (tax payable is ) would show this variance (compensatory in nature).

V. Changes in Table 8 Table 8A details –

Includes:

• ITC of invoices pertaining to FY 2024–25 appearing in GSTR-2B of FY 2024–25
• ITC of invoices pertaining to FY 2024–25 appearing in GSTR-2B of FY 2025–26

Excludes:

• ITC of invoices pertaining to FY 2023–24 appearing in GSTR-2B of FY 2024–25

Note:

Accordingly, Table 8A will remain unchanged as on 1st December 2025. Hence, it is advisable to

file Annual Returns only after this date to ensure completeness and accuracy of ITC reporting.

Domestic ITC – Table 8C

This table covers GSTR-2B credits of the current financial year that are claimed in the

subsequent year. Due to the introduction of Table 6A(1), the relevance of Table 8C has now reduced.

Illustration:

ITC pertaining to FY 2024-25 (as per GSTR-2B) is re-claimed in FY 2025-26 (in GSTR-3B). Such credit was originally claimed, temporarily reversed in FY 2024-25, and subsequently re-claimed in FY 2025-26 (within the prescribed time limit).

Disclosure in GSTR-9:

• For FY 2024-25: Table 6B, Table 6H, and Table 7H (temporary reversal)
• For FY 2025-26: Table 6A(1)

Imported Goods – Table 8H(1)

A new table 8H(1) has been introduced to capture ITC relating to imported goods appearing

in GSTR-2B of the current year but claimed in the next financial year.

Earlier, ITC disclosures were aligned with GSTR-2B irrespective of the year of claim to avoid disputes relating to ITC on import of goods.

Note:

The time limit under Section 16(4) is disputable in the case of ‘Bill of Entry’ documents since the provision specifically applies only to invoices and debit notes.

Form GSTR-9C – Reconciliation Statement

Key Updates

1. Table 7D1 – New Disclosure:

Introduced for supplies on which tax is payable by the e-commerce operator (ECO)

under Section 9(5). These supplies, reported by the supplier, will not form part of taxable turnover.

2. Table 9K2 – New Disclosure:

Introduced for reporting by ECO in respect of supplies taxable under Section 9(5).

3. Table 5B – Turnover Reconciliation:

Unbilled revenue at the beginning of the year can now be merged and disclosed under

Table 5O.

4. Turnover Reconciliation (Tables 5C to 5N):

Each item must be reported separately and cannot be clubbed under Table 5O.

(Note: The relaxation for combined disclosure in Table 5O was available only up to FY 2021-22.)

5. Tables 12B & 12C – Mandatory Disclosure:

From FY 2023-24 onwards, furnishing details in these tables is compulsory.

6. Table 14 – Optional:

Disclosure of expense-wise ITC claim remains optional. (This data is also captured in

Clause 44 of Form 3CD – Tax Audit Report.)

Note 1: Filing of all GSTR-1 and GSTR-3B returns for FY 2024-25 is a prerequisite before filing GSTR-9 and 9C.

Note 2: GSTR-9 and 9C cannot be revised once filed – it is advisable to file them together.

Advanced Issues & Practical Considerations

1. Rule 37A Compliance:

Merely ensuring vendor GSTR-1 filing is no longer sufficient. Vendors must also file GSTR-3B to make ITC eligible for the recipient (Rule 37A, introduced in Dec 2022 read with Section 16(2)(c)).

• Vendor 3B filing status is available in GSTR-2A.
• ITC reversed under Rule 37A can be reclaimed once the vendor files GSTR-3B (disclosed under Table 7A1).
• In practice, such reversals are now rare due to system restrictions allowing GSTR-1 filing only after GSTR-3B submission and automated DRC-01B tracking.

2. Credit Note Disclosure:

The heading in Table 4 of GSTR-9 (“Transactions for the year”) often leads to confusion. Credit notes issued in the next financial year (within permissible timelines) should not be included in the previous year’s return. They must be disclosed in the year in which they are raised.

3. Deferred ITC Ledgers:

Due to GSTR-2B-based ITC restrictions, certain eligible credits may remain unclaimed and recorded in deferred ITC ledgers.

• Such ITC claimed between 1st Apr to 30th Nov 2025 should be disclosed in Table 13 of GSTR-9.
• In GSTR-9C, the entire ITC as per books appears in Table 12A, while Table 12C should reconcile with Table 13 of GSTR-9.
• ITC claimed in subsequent years should appear in Tables 6A1, 6B, and 6H of GSTR-9, and Table 12B of GSTR-9C.

4. Table 8C vs. Table 13 (GSTR-9): Key Differences

a. Table 13 includes ITC on imports and inward supplies under reverse charge — not to be reported in Table 8C.

b. Goods/services in transit (invoiced in current FY but received in next FY) — reported in 8C, not in 13.

c. Invoices accounted in current FY but reflected in GSTR-2B and claimed in next FY — reported only in Table 13.

5. Table 8K – Lapsed ITC Analysis:

Reporting ITC as “lapsed” does not mean automatic debit from the electronic credit ledger; it serves as an indication for departmental settlement (as clarified in July 2019 press release).

However, given recent ITC-related table revisions for FY 2024-25, renewed attention to Table 8K may be required.

6. Negative ITC in Table 4C of GSTR-3B:

Negative ITC (indicating additional tax liability) should be manually included in Table 9

of GSTR-9 for tax reconciliation, as it does not auto-populate.

This will correspondingly affect Table 9 of GSTR-9C. Alternatively, reasons for the

variance can be explained in remarks without manual adjustment.

7. Table 7E vs. Table 9 (GSTR-9C):

Although not a mandatory reconciliation, this cross-check ensures that taxable value as

per books (rate-wise) matches with values reconciled in earlier tables.

Table 9 of GSTR-9C must reflect figures strictly as per books, irrespective of disclosures

in GSTR-3B or GSTR-9.

Disclosure of Additional Liabilities

a. Outward/RCM Liability:

• May be reported in Table 4 of GSTR-9, flowing to Table 9, and supported by DRC-03 payment.
• Alternatively, such liability can be reported directly in Table 9 of GSTR-9C with reference to DRC-03.

b. ITC Reversal or Excess Claim:

• Disclose under Table 7 of GSTR-9.
• Manual addition in Table 9 (tax payable) not needed if variance already reflected in Table 12F of GSTR-9C with DRC-03 reference.

c. Alternate Disclosure:

• Use Part V of GSTR-9C – “Additional Liability due to Non-Reconciliation” for summarizing any remaining differences.

Dos & Don’ts while filing GSTR 9 & 9C?

Do’s

• File GSTR 9 & 9C in time – One of the most basic compliances is filing GSTR 9 & 9C within the due date, which will help the taxpayer to avoid interest, late fees, and notices from the department.
• Maintain 9 & 9C workings with links to all the relevant data. Avoid keyed-in workings.
• Fill accurate data – There are a lot of fields to be filled in while filing the GSTR 9 & 9C. The GSTN does not allow for the amendment of the return once it is filed, this causes hardships to taxpayers, caution to be taken at the time of data entry.
• Perform invoice level reconciliations – A very beneficial exercise to taxpayers, which will help not only in the process of filing the annual return but also to identify the errors.
• Maintain ITC register with capital goods bifurcation so that it will be helpful while preparing table 6 of GSTR 9.
• Maintain the details of ITC claimed, reversed, and re-claimed if the taxpayer fulfils the conditions mentioned u/s 16.
• In case of amendments, outward register to be maintained with original values, so that it will be helpful while table 4 & 5 of GSTR 9.
• Perform reconciliations on monthly basis or at least for every quarter between books and returns.
• Rule 42 & 43 ITC reversals to be made and annual re-computation ITC reversal u/r 42 to be performed before September month return filing to avoid interest liability or missing out ITC.
• Invoice level 2B reconciliation is to be performed for Table 8 disclosure in GSTR-9.
• Maintain advance and advance adjustment workings so that it will be helpful while preparing table 5 of GSTR 9C.

Don’ts

• Don’t forget to file nil return – This is a very important aspect that taxpayers sometimes tend to ignore. If a business does not have any transactions for the entire financial year, a user should not forget to file a NIL return for that FY.
• Do not link any of the 9C tables (other than GSTR-9 values itself) to GSTR-9 tables.
• Do not file without verification, as the returns cannot be revised.