Filing GSTR-3B and Paying the Tax

GSTR-3B began in 2017 as a stop-gap summary that the taxpayer typed in by hand. It is now largely filled in for the taxpayer before it is opened. Liability comes from the taxpayer’s own GSTR-1 and GSTR-1A and, since the July 2025 tax period, cannot be edited. Credit comes from the GSTR-2B shaped by the taxpayer’s actions in the Invoice Management System. Interest for a late return is computed by the portal and placed in the next month’s return. What is left to the filer is the part the portal cannot see: credit to be reversed or reclaimed, reverse charge on imports of services, the breakup of tax that relates to earlier months, and the payment itself.

This guide covers the procedure under section 39 of the CGST Act and rule 61. The law is explained in GSTR-1 and GSTR-3B and the three electronic ledgers. Where GSTR-3B sits in the month is in the returns calendar.

What to have ready

• The period’s GSTR-1, filed, and any GSTR-1A, filed (portal). Section 39(10) bars GSTR-3B until the GSTR-1 is in. A GSTR-1A saved but not filed also blocks GSTR-3B.
• The final GSTR-2B for the period (portal), recomputed after any IMS action taken after the 14th.
• Credit to be reversed (books): under rules 38, 42 and 43, under section 17(5), under rule 37A (shown in the September GSTR-2B), and any temporary reversal.
• Credit to be reclaimed (books, and the portal’s Electronic Credit Reversal and Re-claimed Statement): credit reversed earlier in table 4(B)(2) and now eligible again.
• Reverse charge liability (books, GSTR-2B and the portal’s RCM Liability/ITC Statement), including tax on imports of services and on purchases from unregistered persons that GSTR-2B does not show.
• Exempt, nil-rated, non-GST and composition purchases (books), inter-State and intra-State, for table 5.
• Supplies relating to earlier periods (books, and GSTR-1 document dates), for the “Tax Liability Breakup, As Applicable” table.
• Ledger balances (portal): electronic cash ledger, electronic credit ledger, electronic liability register, and the negative liability statement.
• Any open intimation in FORM GST DRC-01B (rule 88C) or DRC-01C (rule 88D) (portal).
• Funds for the cash portion of the liability, and a working DSC or EVC.

Who files, and by when

Rule 61(1) requires GSTR-3B from every registered person other than an Input Service Distributor, a non-resident taxable person, a supplier of online information and database access or retrieval services from outside India under section 14 of the IGST Act, a composition taxpayer, a tax deductor and an e-commerce operator collecting tax. Casual taxable persons file it.

• Monthly filers: by the 20th of the following month (rule 61(1)(i)).
• QRMP filers: once a quarter, by the 22nd or 24th of the month after the quarter, according to the State of the principal place of business (rule 61(1)(ii)). For the first two months of the quarter they deposit tax in FORM GST PMT-06 by the 25th (rule 61(3)). That deposit is covered in the QRMP guide.

The Commissioner may extend the date under section 39(6), and has done so for particular months or districts. Recent examples are Notification No. 12/2025-Central Tax (July 2025, five Maharashtra districts, to 27 August 2025), Notification No. 17/2025-Central Tax (September 2025 and the July–September 2025 quarter, to 25 October 2025) and Notification No. 01/2026-Central Tax (March 2026, to 21 April 2026).

Section 39(7) requires the tax due on the return to be paid by the last date for filing it. Section 39(8) requires a return for every period, whether or not there were supplies. A nil return can be filed online or by SMS (nil returns).

The tables

The form’s tables, as amended by Notification No. 14/2022-Central Tax (which added table 3.1.1 and recast table 4) and Notification No. 12/2024-Central Tax (which recast table 6.1 and omitted table 6.2, both with effect from 11 February 2025 under Notification No. 09/2025-Central Tax), are set out below. The copy of FORM GSTR-3B on CBIC’s site shows the 2024 changes to table 6 but not the 2022 changes to tables 3 and 4. The portal uses the amended form.

3.1 Outward supplies and inward supplies liable to reverse charge (other than those in 3.1.1):

• (a) outward taxable supplies, other than zero-rated, nil-rated and exempt
• (b) zero-rated supplies (exports and supplies to SEZ)
• © nil-rated and exempt supplies
• (d) inward supplies liable to reverse charge
• (e) non-GST outward supplies

3.1.1 Supplies notified under section 9(5), for services where the e-commerce operator pays the tax:

• (i) is filled by the operator
• (ii) is filled by the supplier selling through the operator, which reports only the taxable value here and leaves it out of 3.1(a)

3.2 Inter-State supplies to unregistered persons, composition taxpayers and UIN holders, out of 3.1(a) and 3.1.1(i), by place of supply.

4 Eligible ITC:

• (A) ITC available: (1) import of goods, (2) import of services, (3) inward supplies liable to reverse charge other than (1) and (2), (4) from Input Service Distributors, (5) all other ITC.
• (B) ITC reversed: (1) as per rules 38, 42 and 43 and section 17(5); (2) others, including rule 37A reversals and temporary reversals.
• © Net ITC available: (A) minus (B).
• (D) Other details: (1) ITC reclaimed which was reversed under table 4(B)(2) in an earlier period; (2) ineligible ITC under section 16(4) and ITC restricted by place of supply provisions.

5 Exempt, nil-rated and non-GST inward supplies, inter-State and intra-State, including purchases from composition suppliers.

5.1 Interest and late fee for the previous tax period.

6.1 Payment of tax. For each head, separately for (A) liabilities other than reverse charge and section 9(5), and (B) reverse charge and section 9(5): tax payable, adjustment of negative liability of a previous period, net tax payable, tax paid through ITC (by head), tax paid in cash, interest paid in cash, and late fee paid in cash.

On reclaimed credit, GSTN’s advisory of 29 December 2025 says the credit reversed in 4(B)(2) is reclaimed by showing it in 4(A)(5) and also in 4(D)(1). The portal tracks both in the reclaim statement.

What fills itself, and what is locked

The portal’s GSTR-3B FAQs set out the auto-population:

GSTR-3B table	Source
3.1(a), (b), ©, (e) and 3.2	GSTR-1 and GSTR-1A (tables 4 to 11, net of credit notes and amendments)
3.1.1(i) and (ii)	GSTR-1 and GSTR-1A tables 15 and 14
3.1(d)	GSTR-2B reverse charge sections
4(A)(1), (3), (4), (5)	GSTR-2B, net of credit notes
4(D)(2)	GSTR-2B “ITC not available”
5.1	System-computed interest and late fee on the previous return
4(A)(2), 4(B), 4(D)(1), 5	Entered by the taxpayer

Liability is locked. GSTN’s advisory of 7 June 2025 states that from the July 2025 tax period, for which GSTR-3B is filed in August 2025, the liability auto-populated from GSTR-1, GSTR-1A and IFF “will become non editable”. Taxpayers “will be allowed to amend their auto populated liability by making amendments through form GSTR 1A”, before filing GSTR-3B. This followed an advisory of 17 October 2024 announcing the change for the January 2025 period, and one of 27 January 2025 deferring it. A further advisory of 5 December 2025 made table 3.2 non-editable from the November 2025 period. A value auto-populated wrongly in 3.2 is corrected through GSTR-1A, which “shall change the auto-populated values of table 3.2 in GSTR-3B instantly”.

Three points on the lock:

• Its legal basis is thin. From 1 October 2025, section 128 of the Finance Act, 2025 amended section 39(1) so that the return is furnished “within such time, and subject to such conditions and restrictions, as may be prescribed”. No rule yet prescribes the lock. On 8 October 2026 the GST Council recommended inserting sub-rule (1A) in rule 61 to provide a mechanism for “correct reporting and correction/rectification of liability in the return”, and sub-rule (1B) to do the same for credit. It proposed that these apply from the return for April 2027.
• Credit is not locked. GSTN’s October 2024 advisory said locking of auto-populated ITC “will be implemented from a later date”, and no later advisory has done so. Credit in table 4 can still be edited, but a claim above GSTR-2B beyond the notified limit draws an intimation in FORM GST DRC-01C under rule 88D. The portal also checks credit against the two statements. Reclaimed credit in 4(D)(1) may not exceed the reclaim statement balance plus the current period’s 4(B)(2) reversal. Reverse charge credit in 4(A)(2) and 4(A)(3) may not exceed the RCM statement balance plus the tax paid in 3.1(d). GSTN’s advisory of 29 December 2025 announced that these checks would become blocking “shortly”, and the GSTR-3B user manual already says the return cannot be filed while RCM statement entries for the previous period are unposted.
• The portal’s own help is out of date. The GSTR-3B FAQs (question 7) and the user manual still say the auto-populated values “are kept editable”, with a red highlight and a warning. They have not been revised for the June and December 2025 advisories.

The comparison between GSTR-1 and GSTR-3B also continues under rule 88C. Where the tax in GSTR-1 (as amended in GSTR-1A) or IFF exceeds that in GSTR-3B beyond the notified limit, an intimation in FORM GST DRC-01B follows.

The liability register and DRC-03

Every liability is recorded in the electronic liability register in FORM GST PMT-01 under rule 85. It covers tax, interest and late fee as per the return, and amounts determined by an officer or ascertained by the taxpayer. A GSTR-3B debits it with the period’s liability and credits it on payment. Where tax is found short after filing, it is paid through FORM GST DRC-03, not by revising the return. That route, and the portal’s negative liability statement used in table 6.1, are covered in correcting mistakes in returns.

Paying: the cash ledger and the challan

Tax is paid only by debiting the electronic cash ledger or the electronic credit ledger. Rule 61(2) requires the liability to be discharged “by debiting the electronic cash ledger or electronic credit ledger” and the details included in the return.

Cash reaches the cash ledger, FORM GST PMT-05, through a challan under rule 87:

• The challan. FORM GST PMT-06 is generated on the portal. It is valid for fifteen days (rule 87(2)).
• Modes of payment. Internet banking through authorised banks; UPI and IMPS from any bank; credit or debit card; NEFT or RTGS from any bank, with a mandate form generated with the challan and valid for fifteen days; and over the counter at authorised banks for up to Rs 10,000 per challan per tax period, by cash, cheque or draft (rule 87(3)).
• When payment counts. The bank generates a Challan Identification Number (CIN) and the amount is credited to the cash ledger (rule 87(6), (7)). The date of deposit is “the date of credit to the account of the Government in the authorised bank” (Explanation to section 49).
• Problems. Where the bank account is debited but no CIN reaches the portal, the taxpayer represents in FORM GST PMT-07 (rule 87(8)).
• Wrong head. Cash paid under the wrong head can be transferred to another head, or to a distinct person’s integrated or central tax cash ledger, in FORM GST PMT-09. The transfer to a distinct person is barred while any liability is unpaid in the liability register (rule 87(13), (14)).

From the GSTR-3B payment screen, where cash is short, the portal offers to create a challan. The portal’s user manual describes the challan amount as auto-populated and not editable there. The payment mode is chosen and GENERATE CHALLAN clicked.

Setting off: which ledger pays what

The set-off rules are explained in the guide on the three electronic ledgers. In outline:

• What credit can pay. The credit ledger pays only output tax (section 49(4)). Reverse charge tax, interest, late fee and penalty are paid in cash (rule 85(4)). The portal also requires cash for tax on section 9(5) supplies reported by an operator in 3.1.1(i).
• Integrated tax credit first. It pays integrated tax, and the balance pays central tax and State or Union territory tax “in any order”. Central and State credit can be used only after integrated tax credit is fully used (rule 88A; section 49A).
• No crossing. Central tax credit may not pay State or Union territory tax, and State or Union territory tax credit may not pay central tax (section 49(5)(e), (f)).
• Arrears first. Section 49(8) applies payments first to self-assessed tax and dues of earlier periods, then to the current period, then to other amounts including demands.
• One per cent in cash. Where rule 86B applies, at least one per cent of output tax is paid in cash.

The portal’s user manual adds that the offset “is available only once for use in a tax period” and cannot be done in part. The whole liability must be offered for set-off together.

Interest on the net cash liability

Section 50(1) imposes interest on tax paid late, at the rate notified. Notification No. 13/2017-Central Tax fixes 18 per cent a year. The proviso, substituted by the Finance Act, 2021 with effect from 1 July 2017, limits interest where the supplies of a period are declared in that period’s return but the return is filed late. Interest is then “levied on that portion of the tax that is paid by debiting the electronic cash ledger”. This does not apply where the return is filed after proceedings under section 73, 74 or 74A have begun for the period.

Rule 88B(1) applies the proviso. Its own proviso, inserted by Notification No. 12/2024-Central Tax from 10 July 2024, goes further. Cash credited to the cash ledger on or before the due date, and lying there from the due date until it is debited in the late return, is left out of the calculation. In all other cases, including tax of an earlier period paid in a later return, rule 88B(2) charges interest on the whole tax unpaid, from the day after it fell due until payment.

The portal applies this in three steps:

• Computing. It computes the interest after a late GSTR-3B is filed, and places it in table 5.1 of the next GSTR-3B. This is the same way the late fee is collected. From the January 2026 period it gives the benefit of the minimum cash balance between the due date and the date of debit, using the formula in GSTN’s advisory of 30 January 2026: “(Net Tax Liability – Minimum Cash Balance in ECL from due date to date of debit) × (No. of days delayed / 365) × Applicable Interest Rate”.
• Earlier periods. Tax relating to supplies of earlier periods attracts interest on the gross amount. The taxpayer declares it in the “Tax Liability Breakup, As Applicable” table on the payment page. From the February 2026 period the portal fills that table from the document dates in GSTR-1, GSTR-1A and IFF, and the taxpayer must confirm or edit it before filing. At present the portal asks for confirmation in every case (GSTN advisory of 16 March 2026).
• Editing. The January 2026 advisory makes the system figure in table 5.1 the minimum. It can be raised but not lowered. After errors in the February 2026 figures, a RE-COMPUTE INTEREST button was added. The taxpayer may edit table 5.1 to the recomputed figure, but not below it (advisory of 16 April 2026). Interest on a late final GSTR-3B of a cancelled taxpayer is collected in GSTR-10.

Interest on credit “wrongly availed and utilised” falls under section 50(3) and is calculated under rule 88B(3).

Late fee

Section 47(1) imposes a late fee of Rs 100 a day, up to Rs 5,000. Notification No. 76/2018-Central Tax, as amended by Notification No. 19/2021-Central Tax, waives the central fee above these amounts, for periods from June 2021 (or the quarter ending June 2021):

Class	Fee per day (central tax)	Maximum (central tax)
Central tax payable in the return is nil	Rs 10	Rs 250
Aggregate turnover up to Rs 1.5 crore	Rs 25	Rs 1,000
Over Rs 1.5 crore and up to Rs 5 crore	Rs 25	Rs 2,500
Over Rs 5 crore	Rs 25	Rs 5,000 (section 47)

The portal’s user manual computes the fee “per Act (CGST/SGST)”, so an equal amount is payable under the State or Union territory Act. It charges no late fee on integrated tax or cess, and treats a negative liability as nil. The fee is computed after the late return is filed and collected in table 5.1 of the next GSTR-3B. It is paid only in cash. The waiver for taxpayers with turnover up to Rs 5 crore who file within the month, recommended by the Council on 8 October 2026, is not yet notified.

Filing on the portal

The portal’s GSTR-3B user manual describes these steps:

1. The taxpayer goes to Services > Returns > Returns Dashboard, selects the period and clicks PREPARE ONLINE in the GSTR-3B tile. The SYSTEM GENERATED GSTR-3B button gives a PDF of the auto-populated values with their breakup.
2. Tile by tile, it confirms table 3.1, 3.1.1 and 3.2, enters the table 4 reversals, reclaims and import of services credit, enters table 5, and checks table 5.1. Each tile is closed with CONFIRM. A NAVIGATE TO GSTR-1A link leads to GSTR-1A where liability needs correcting.
3. SAVE GSTR3B, then PREVIEW DRAFT GSTR-3B to check.
4. PROCEED TO PAYMENT shows cash and credit available, the negative liability adjustment, and the cash still required. It also offers TAX LIABILITY BREAKUP, AS APPLICABLE, which the taxpayer opens and saves.
5. If cash is short, the taxpayer creates a challan and pays. Then MAKE PAYMENT/POST CREDIT TO LEDGER sets off the liability.
6. PROCEED TO FILE, a declaration, the authorised signatory, and FILE GSTR-3B WITH DSC or FILE GSTR-3B WITH EVC. The portal issues an acknowledgement reference number.

Signing

Rule 26 allows a digital signature certificate, e-signature, or a mode notified by the Board. Notification No. 6/2017-Central Tax notifies electronic verification code. The proviso that required companies to use a DSC has been omitted since 1 November 2021 (Notification No. 32/2021-Central Tax), and the portal treats DSC as optional for all. Rule 26(2) names the signatory. For a company, it is the chief executive officer or authorised signatory; for a firm, any adult partner or authorised signatory; for an HUF, the karta.

What can be changed after filing

A filed GSTR-3B cannot be revised. Under section 39(9), an omission or incorrect particular found by the taxpayer, other than as a result of scrutiny, audit, inspection or enforcement, is rectified in the return for the period in which it is noticed, with interest. No rectification is allowed after 30 November following the end of the financial year, or the date of the annual return, if earlier. Section 39(11) bars filing a GSTR-3B more than three years after its due date, and the portal has applied that bar since 1 December 2025. Short payment found later is paid through DRC-03. Liability errors in the current period are corrected in GSTR-1A before filing. These routes are covered in the guide on correcting mistakes, linked above, and in the guide on late returns.

The procedure in order

1. File the period’s GSTR-1, and any GSTR-1A, and recompute GSTR-2B after final IMS actions.
2. Open GSTR-3B and check the auto-populated liability. Correct it through GSTR-1A, not in GSTR-3B.
3. Check the auto-populated credit. Enter reversals in 4(B), reclaims in 4(A)(5) and 4(D)(1), import of services in 4(A)(2), and table 5.
4. Check table 5.1 against the previous return’s lateness, recomputing interest if needed.
5. Proceed to payment and confirm the tax liability breakup for earlier-period supplies.
6. Deposit any cash shortfall by PMT-06, then offset the whole liability: integrated credit first, no central–State crossing, cash for reverse charge, interest and fees.
7. File with DSC or EVC by the 20th, or the 22nd or 24th for a quarter.
8. Answer any DRC-01B or DRC-01C intimation within seven days.

The next guide covers the QRMP scheme: quarterly returns, the Invoice Furnishing Facility, and monthly payment in FORM GST PMT-06.