GST Return Filing Guide: GSTR-1, GSTR-3B and GSTR-9

Every registered business files GST returns, even in a month with no sales. The system has tightened considerably since 2025: the tax figures in GSTR-3B are now locked to what you report in GSTR-1, input tax credit is driven by GSTR-2B and the Invoice Management System (IMS), and returns more than three years overdue can no longer be filed at all. Here is how it fits together.

The main returns

Return	What it is	Who files
GSTR-1	Details of outward supplies (sales): B2B invoice-wise, B2C summary, exports, credit and debit notes	All regular taxpayers
IFF (Invoice Furnishing Facility)	Optional upload of B2B invoices for the first two months of a quarter	QRMP taxpayers
GSTR-1A	Amends the current period’s GSTR-1 before filing GSTR-3B	Optional
GSTR-3B	Summary return with tax payment: output tax, ITC claimed, net tax paid	All regular taxpayers
GSTR-2B	Auto-drafted ITC statement based on suppliers’ GSTR-1/IFF, after your IMS actions	System-generated (no filing)
CMP-08 / GSTR-4	Quarterly payment and annual return	Composition taxpayers
GSTR-9	Annual return	Regular taxpayers (optional up to ₹2 crore turnover)
GSTR-9C	Reconciliation statement (self-certified)	Turnover above ₹5 crore

Due dates

Monthly filers

Return	Due date
GSTR-1	11th of the next month
GSTR-3B	20th of the next month

QRMP scheme (turnover up to ₹5 crore)

Return / payment	Due date
IFF (months 1 and 2, optional)	13th of the next month
PMT-06 tax payment (months 1 and 2)	25th of the next month
GSTR-1 (quarterly)	13th after the quarter
GSTR-3B (quarterly)	22nd or 24th after the quarter, depending on the state. Maharashtra is in the 22nd group

Annual

Return	Due date
GSTR-9 / 9C	31 December after the financial year (31 Dec 2026 for FY 2025-26)

Due dates are often extended by notification. Check the GST portal before each deadline.

Late fees and interest

Default	Consequence
Late GSTR-3B / GSTR-1	₹50 per day (₹25 CGST + ₹25 SGST). ₹20 per day for nil returns. Capped (for GSTR-3B) at ₹500 for nil returns, ₹2,000 for turnover up to ₹1.5 crore, ₹5,000 for ₹1.5–5 crore and ₹10,000 above ₹5 crore
Late GSTR-9	₹50 per day (turnover up to ₹5 crore, capped at 0.04% of turnover), ₹100 per day (₹5–20 crore, capped at 0.04%), ₹200 per day (above ₹20 crore, capped at 0.5%)
Late payment of tax	Interest at 18% a year on the net cash liability
Wrong ITC availed and utilised	Interest at 24% a year

Late GSTR-3B also blocks your GSTR-1 for the next period, and continued non-filing can lead to cancellation of registration.

The 2025–26 changes you must know

GSTR-3B liability is hard-locked. From the July 2025 tax period, the output tax auto-filled from GSTR-1/IFF/GSTR-1A cannot be edited in GSTR-3B. To correct sales figures, amend through GSTR-1A before filing GSTR-3B, or in the next GSTR-1.
Invoice Management System (IMS). Since October 2024, recipients can accept, reject or keep pending each supplier invoice on IMS. Your action decides what flows into GSTR-2B, and so how much ITC you can claim. A further phase linking the GSTR-3B ITC table to GSTR-2B is being rolled out. Check the latest GSTN advisory.
Three-year time bar. Under the Finance Act 2023 amendment, operational on the portal since 2025, GSTR-1, GSTR-3B, GSTR-9 and other returns cannot be filed after three years from their original due date. Old unfiled returns are lost for good, along with the ITC.
Rate rationalisation (GST 2.0). From 22 September 2025, most goods and services moved into 5% and 18% slabs, with a 40% rate for specified luxury and sin goods. Update the rates in your billing software.

Nil returns

If there were no sales, purchases or tax liability for the period, file a nil GSTR-1 and nil GSTR-3B. This can be done by SMS to 14409, or on the portal in a few clicks. Missing a nil return still attracts a late fee.

A monthly routine that works

Close the month’s books by the 5th.
Review supplier invoices on IMS: accept, reject or keep pending.
File GSTR-1 by the 11th. Check that B2B invoices have the correct GSTINs.
Reconcile GSTR-2B with your purchase register and follow up on missing supplier invoices.
File GSTR-3B by the 20th and pay the tax in cash and through ITC.
Keep a monthly reconciliation file. It will make GSTR-9 and audits much easier.

Frequently asked questions

Can I revise a GSTR-3B?
No. GSTR-3B can’t be revised. Corrections are made in later returns, and output tax changes must go through GSTR-1/GSTR-1A, because the 3B liability is now locked.

Is GSTR-9 compulsory for small taxpayers?
It is optional for taxpayers with aggregate turnover up to ₹2 crore, subject to the government’s annual notification.

What if I haven’t filed returns for many months?
File the oldest pending returns immediately, before they cross the three-year limit. If registration has been cancelled for non-filing, apply for revocation after filing the pending returns.

Behind on GST returns or struggling with IMS and GSTR-2B? Garvita Jain & Co. handles monthly or quarterly GST filing, IMS actions and ITC reconciliation, GSTR-9/9C, and catch-up filing for missed periods. Contact us here, or at contact@garvitajainandco.com or +91 98678 16597.

This article is general information based on the law as of November 2026 and is not professional advice.

Sources

Official

Professional / CA publications