GSTR-3B vs GSTR-1: what a Pvt Ltd director must know about due dates, penalties, and the ITC linkage

GSTR-1 is due monthly by the 11th (quarterly by the 13th under QRMP) and GSTR-3B by the 20th — and filing one without the other does not just invite a ₹50-per-day late fee, it blocks your buyers' input tax credit. The ITC a recipient claims in GSTR-3B must appear in GSTR-2B, which is generated from your GSTR-1. Under s.16(2)(aa) CGST Act 2017, an invoice you never filed is credit your customer cannot lawfully take.

What the law actually requires

GSTR-1 (outward supplies) is filed under s.37 CGST Act 2017 read with Rule 59; GSTR-3B (summary return and tax payment) under s.39(1) read with Rule 61. The two serve different masters: GSTR-1 feeds your buyers' GSTR-2B, GSTR-3B settles your cash tax liability.

Who files monthly vs quarterly. A taxpayer with aggregate turnover above ₹5 crore in the preceding FY must file both GSTR-1 and GSTR-3B monthly. Turnover up to ₹5 crore can opt into the QRMP scheme — GSTR-1 and GSTR-3B go quarterly, but tax still flows every month through Form GST PMT-06 by the 25th, so the government's cash is never deferred.

The ITC linkage. GSTR-2B is an auto-generated statement of your inward supplies, built entirely from your suppliers' GSTR-1 (and GSTR-5/6/7 and import data). You do not file it; you reconcile against it. The chain is statutory: s.16(2)(aa) CGST Act 2017 provides that ITC is available only if the supplier has furnished the invoice details in its outward-supply statement and they have been communicated to you. That means: no supplier GSTR-1 → no invoice in your GSTR-2B → no ITC in your GSTR-3B. Rule 36(4) is the safety valve — provisional credit for invoices not yet in GSTR-2B is capped at 5% of the eligible credit that is in GSTR-2B.

Late fee (s.47). The fee is ₹50 per day (₹25 CGST + ₹25 SGST), ₹20 per day for nil returns, capped at ₹10,000 per return for GSTR-3B and ₹5,000 for GSTR-1. Interest (s.50) is separate and steeper: 18% per annum on the tax paid after the due date, from the due date to the date of payment.

What changed FY 2025-26

• ITC deadline is now 30 November, not September. Under s.16(4) as amended by the CGST (Amendment) Act 2022, ITC for FY 2025-26 must be claimed in a GSTR-3B filed on or before 30 November 2026. A supplier's late GSTR-1 that pushes your invoice into GSTR-2B after that date can cost you the credit permanently — the recipient bears the supplier's lateness.
• GSTR-2B is the reconciliation anchor. With the 5% provisional cap in Rule 36(4) fully operative, a company that claims full credit while 10% of its purchases are missing from GSTR-2B is carrying an excess that auto-flagging will catch.
• Nil-return and enforcement messaging. The department's late-fee waivers for pandemic-period returns have ended; the standard s.47 scale applies to every return from FY 2025-26 onward. GSTN also strengthened email/SMS nudges so a skipped return is harder to plead as "overlooked."

Worked example: Riya Pvt Ltd delays its October GSTR-1

Riya Pvt Ltd is a monthly filer in Karnataka with turnover above ₹5 crore. It files GSTR-1 for October 45 days late and pays its October tax 10 days after the due date of GSTR-3B.

The bigger cost is downstream. Riya's B2B customers file their November GSTR-3B on 20 December; Riya's October invoices are not yet in their GSTR-2B, so under s.16(2)(aa) they cannot claim the corresponding ITC that month. If Riya's October invoices carried ₹3,00,000 of GST for one customer, that customer's working capital is locked out of ₹3,00,000 of credit until a later return — and if the invoices land after that customer's 30 November 2026 s.16(4) deadline, the credit is gone permanently.

What a director should actually watch

• Calendar the 11th, 13th, 20th, 22nd/24th and 25th as five different dates. One monthly reminder for "GST" fails in practice; QRMP companies have three obligations a month, not one.
• Reconcile GSTR-2B to GSTR-3B before you press "file". Table 4(A) of GSTR-3B should not exceed eligible credit per GSTR-2B plus the 5% Rule 36(4) provisional margin.
• Track the two-month matching window. An invoice that appears in GSTR-2B but was never reflected in your purchase register indicates a supplier who filed late or omitted the document — follow up before your own s.16(4) clock runs.
• Treat GSTR-1 as a customer-facing document. A late GSTR-1 is your customers' cash-flow problem; in practice they will stop buying from a supplier who routinely files late rather than absorb blocked credit.

FAQ

Can we file GSTR-3B without filing GSTR-1?
Yes, the portal allows it, but it is an error: GSTR-3B is a self-declared summary, so it files without GSTR-1. Your buyers' GSTR-2B stays empty for that period, their ITC is blocked under s.16(2)(aa), and the turnover mismatch between GSTR-1 and GSTR-3B is exactly what the annual reconciliation in GSTR-9C flags.

Is the late fee the same for a nil return?
No. A nil GSTR-1 or GSTR-3B attracts ₹20 per day (₹10 CGST + ₹10 SGST), capped at ₹5,000 for GSTR-1 and ₹10,000 for GSTR-3B. Nil status means all tables zero — a return showing only exempt sales is not nil for fee purposes in most states.

Does interest under s.50 apply if tax was paid on time but the return was late?
No, not on the tax — the Supreme Court's reading of s.50(1) is that interest runs only on tax not paid by the due date. But the late fee under s.47 still applies to the return, and under s.50(3) interest at 18% applies where ITC was wrongly availed and utilised.

What is the 5% provisional ITC rule, practically?
If your GSTR-2B shows eligible credit of ₹10,00,000, you may claim up to ₹10,50,000 in GSTR-3B — the extra ₹50,000 being credit on invoices not yet in GSTR-2B. Claim ₹11,00,000 and ₹50,000 is excess credit attracting 18% interest under s.50(3) when utilised.

For a GST return compliance calendar for your company, visit pvtltd.co.

Sources

• s.37, s.39(1), s.47, s.50 CGST Act 2017
• s.16(2)(aa), s.16(4) CGST Act 2017 (as amended by CGST (Amendment) Act 2022)
• CGST Rules 59, 61, 36(4) (GSTR-1, GSTR-3B, provisional ITC cap)
• QRMP scheme — Notification 82/2020-CT and 83/2020-CT dated 10 November 2020

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See Also

• GST registration for a Pvt Ltd company: threshold, timeline, and mandatory triggers even below ₹40L
• Annual Return GSTR-9 and GSTR-9C for Pvt Ltd: who must file, what's reconciled, and the ₹5Cr turnover line
• GST on intercompany transactions, director salary, and related-party supplies: what a Pvt Ltd must declare

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