How credit pays a GSTR-3B in the order section 49 and rule 88A fix, where marketplace TCS lands in the cash ledger, and why a draft can differ.
The GSTR-3B is the return that pays the tax
The GSTR-1 says what you sold. The GSTR-3B is the monthly or quarterly return in which the tax on it is paid (section 39(1) of the CGST Act, rule 61 of the CGST Rules and Form GSTR-3B, as amended by Notification 14/2022-Central Tax). Table 3.1 holds outward supplies and inward supplies under reverse charge; 3.1.1 supplies on which an operator pays the tax under section 9(5); 3.2 the inter-state share of those sales made to unregistered buyers, composition dealers and UIN holders, by state; Table 4 the input tax credit; and Table 6.1 the payment.
Most of it arrives filled in. As the GSTN advisory on auto-population of details in Form GSTR-3B from Form GSTR-1 and GSTR-2B (5 December 2020) describes, the portal fills the outward rows of Table 3.1 and Table 3.2 from the GSTR-1 you filed, and 3.1(d) and Table 4 from your GSTR-2B. From the July 2025 period the liability it fills in from the GSTR-1 is locked against overtyping (GSTN advisory on hard-locking of auto-populated liability in GSTR-3B, 7 June 2025), and from the November 2025 period so are the values in Table 3.2 (GSTN advisory on reporting values in Table 3.2 of GSTR-3B, 5 December 2025): a wrong outward figure is corrected through GSTR-1A before the GSTR-3B is filed, or in a later GSTR-1.
What you pay by challan is the tax left once the credit in Table 4(C) has been used in the order the law fixes, plus what credit may never pay, less what is already in your cash ledger, such as the tax your marketplaces collected at source.
Credit pays tax in the order the Act fixes
Sections 49(5), 49A and 49B of the CGST Act and rule 88A of the CGST Rules (Notification 16/2019-Central Tax, from 29 March 2019) set the order. Integrated tax credit goes first against integrated tax, and what remains against central and state tax in any order and proportion. Central or state credit is used only once integrated credit has run out or has nothing left to pay. Central tax credit then pays central tax and then integrated tax; state tax credit pays state tax and then integrated tax; neither ever pays the other. Cess credit pays only cess.
Rule 88A leaves a choice open: where integrated credit left after integrated tax goes. fynxIQ’s draft sends it to whichever of central and state tax its own credit cannot cover, which leaves the least to pay in cash. Credit left over at the end stays in the credit ledger for a later month.
An invented month shows the order. A seller sells ₹60,000 to buyers in other states and ₹20,000 within its own, all at 18 per cent and all through marketplaces. Its GSTR-2B gives ₹7,000 of integrated credit and ₹2,000 each of central and state credit, and nothing is reversed.
- Tax on the month: ₹10,800 integrated, ₹1,800 central, ₹1,800 state.
- Integrated credit against integrated tax: ₹7,000, leaving ₹3,800 of integrated tax.
- Central credit against central tax, and state credit against state tax: ₹1,800 each, leaving ₹200 of each credit.
- The two ₹200 remainders against integrated tax: ₹400, leaving ₹3,400.
- Cash due before TCS: ₹3,400, all of it integrated tax.
Some tax can only be paid in cash
The credit ledger pays output tax and nothing else (section 49(4) of the CGST Act), and output tax leaves out tax payable under reverse charge (section 2(82)). So on supplies notified under section 9(3) (Notification 13/2017-Central Tax (Rate)), where you as the buyer owe the tax, it is paid in cash in Table 6.1 and only then taken as credit in Table 4(A)(3). Imports of services are paid the same way. Interest and late fee are not output tax either, and are paid in cash.
fynxIQ’s draft puts the reverse-charge tax that suppliers marked in your GSTR-2B into 3.1(d) and straight into the cash, never into what credit pays, and shows it as credit in 4(A)(3).
A late GSTR-3B also carries interest. When you file late of your own accord, before any proceedings for the period, interest runs only on the tax paid from the cash ledger, not on what credit paid. The draft works out neither interest nor late fee; both go in Table 5.1 on the portal.
The tax your marketplaces collected is cash, once you accept it
Each marketplace collects tax at source under section 52 on the net value of what you sold through it, and reports it against your GSTIN in its GSTR-8. Section 52(7) of the CGST Act lets you claim that tax, as the operator’s statement shows it, as credit in your electronic cash ledger. It reaches the ledger when you accept it in the portal’s TDS and TCS credit received statement; a row not yet accepted is not in the ledger and pays nothing.
It stays under the head it was collected in: integrated tax on sales to other states, central and state tax on sales within yours. fynxIQ’s draft applies it after credit, to the cash still due, head by head. A head it does not cover is still paid in cash.
In the invented month, at the rate in force since 10 July 2024 (Notification 15/2024-Central Tax and Notification 1/2024-Integrated Tax), the operators collected ₹300 of integrated tax, half a per cent of ₹60,000, and ₹50 each of central and state tax, a quarter per cent of ₹20,000 under each. The ₹300 pays integrated tax, so ₹3,100 is left for the challan. The two ₹50 have nothing to pay, since credit cleared central and state tax, and stay in the ledger. The portal’s form PMT-09 can move a cash balance from one head to another; the draft does not assume you will.
From the portal’s Excel statement the draft counts every row not rejected, takes a restated row as restated and names any amount not yet accepted; from its PDF, which prints only the accepted total, it takes that total.
Where a gap with the portal sits says what caused it
Drop the portal’s own GSTR-3B PDF for the period, draft or filed, beside fynxIQ’s draft. It is read row by row, and the draft is held against it to the paisa in every row of 3.1, the operator row of 3.1.1, the total to unregistered buyers in 3.2 and every row of Table 4 but the net in 4(C), with a rupee allowed on each figure for the portal’s own rounding.
- A gap in 3.1 or 3.2: the GSTR-1 held here is not the one on the portal, or a GSTR-1A changed it. Amendments of earlier months in this GSTR-1 show here too: the portal nets their effect into 3.1, the draft does not.
- A gap in 3.1 in a month when returns exceed sales: the portal shows a negative net as zero, as GSTN’s advisory of 5 December 2020 says, and the draft keeps the negative figure.
- A gap in 3.1(d): imports of services and supplies from unregistered persons under reverse charge, which no statement carries, entered on the portal; or an amended reverse-charge document in the GSTR-2B, which the draft leaves out.
- A gap in 4(A) or 4(D)(2): the GSTR-2B here is for another month, or credit was entered by hand. An amended document in the GSTR-2B is left out of 4(A) and named. 4(A)(2), imports of services, is not computed and is marked so.
- A gap in 4(B) or 4(D)(1): the reversals stated in fynxIQ are not the ones entered on the portal. Until you state yours, the draft’s payable is before reversals and says so.
Every row can agree while the cash still differs
The comparison covers Tables 3 and 4, not the payment. If every row agrees and the portal’s Table 6.1 still asks for different cash, the draft has left out one of these on purpose:
- Credit already in your credit ledger from earlier months. The draft uses only this month’s 4(C), so the portal may ask for less.
- Cash already in your cash ledger: tax collected at source in earlier months, or a PMT-06 deposit. The draft counts only this period’s TCS statement.
- TCS not yet accepted. The draft counts it and names the amount; the ledger holds it only once you accept it.
- Interest and late fee in Table 5.1, which the draft does not work out.
The payment is in whole rupees
Section 170 of the CGST Act rounds every sum payable to the nearest rupee, fifty paise up, and the portal applies it head by head. Tables 3.1 and 4 print paise; Table 6.1 and the ledgers take whole rupees. On one seller’s filed October 2025, the 4(C) credit of ₹1,835.67, ₹3,813.56 and ₹3,813.56 went into the credit ledger as ₹1,836, ₹3,814 and ₹3,814, and the integrated tax of ₹429.11 in 3.1(a) was ₹429 in Table 6.1.
fynxIQ’s draft does the same. Tables 3.1 and 4 stay in paise, as the form prints them. The tax payable, the credit that pays it and the cash left are shown head by head in whole rupees, as Table 6.1 will show them, and the Excel download carries both the paise and the rupees.
On the portal, the challan comes before the offset and the filing
fynxIQ does not pay or file anything. A late GSTR-3B carries its own late fee in Table 5.1, and the portal files the return only once every amount in it, the fee included, has been paid; the free GST late fee calculator works out the figure. A late GSTR-3B also holds up the next GSTR-1: a GSTR-1 cannot be filed while the GSTR-3B for the period before it is unfiled.
A quarterly filer pays the tax of a quarter’s first two months by a PMT-06 challan, with no return (Notification 84/2020-Central Tax, the QRMP scheme). On the portal, the order is fixed:
- Drop the portal’s GSTR-3B PDF on fynxIQ’s GSTR-3B screen and settle every gap before anything is paid.
- Enter what the portal cannot fill for you: the reversals in 4(B), imports of services, and supplies from unregistered persons under reverse charge.
- Go to the payment table, 6.1. It sets the tax against your credit and cash ledgers and shows, head by head, how much more cash is needed.
- Create a challan in form PMT-06 (rule 87 of the CGST Rules) for that amount under each head, and pay it.
- Return to the GSTR-3B and make the payment, which debits both ledgers.
- File with your DSC or EVC and keep the ARN. In a practice workspace, record it against the GSTR-3B on the firm’s board.
In the app, on every plan, the free one included: GSTR-3B draft.
Which file to download, and from where: the list for each marketplace and the GST portal.
By Raunak Pathak, founder of fynxIQ, who files GST returns on it. Last updated 15 October 2026. This is general information about how GST returns work, not advice about your particular return.