How to file GSTR-3B on the GST portal, step by step

Every month, someone in your accounts team sits down with the GST portal open in one tab and Tally or an Excel sheet in the other, trying to make GSTR-3B match the books before the due date. When it goes smoothly, it takes twenty minutes. When it doesn’t, it turns into a late night, a late fee and sometimes a notice a few months later.

This guide walks through the filing the way it actually happens on the portal today, including the parts that are now filled in for you and the order in which you pay and file.

What GSTR-3B is and when it is due

GSTR-3B is the summary return in which you declare your sales, the input tax credit (ITC) you are claiming and the tax you are paying for the period. It is the return through which the tax actually gets paid, so the government watches it closely.

Due dates depend on how you file:

Monthly filers: by the 20th of the following month. The return for March is due by 20 April.
Quarterly filers under QRMP: by the 22nd or 24th of the month after the quarter, depending on your state. You still pay tax for the first two months of the quarter through a challan (PMT-06) by the 25th of the following month.

Late filing attracts a late fee for every day of delay, and tax paid late in cash attracts interest at 18% a year. Your CA can tell you the current late fee caps for your turnover.

Once filed, GSTR-3B cannot be revised. A mistake can only be corrected in a later month’s return, so it is worth spending ten extra minutes checking before you file.

Keep these ready before you log in

Your sales register for the month, matched with what you reported in GSTR-1 (or IFF, if you are a quarterly filer).
Your purchase register, and the GSTR-2B for the month downloaded from the portal. GSTR-2B shows the ITC your suppliers have reported for you.
Details of any reverse charge purchases, such as legal fees or goods transport services where you pay the tax.
Credit notes and debit notes issued or received during the month.
The mobile number or DSC of the authorised signatory, for filing.

A common habit in small firms is to wait for the accountant at month end and then rush. If your billing and purchase entries are posted daily, most of this list is ready by the 10th.

Step 1: Log in and open the return

Go to www.gst.gov.in and log in with your portal username and password (not your GSTIN).
Open Services > Returns > Returns Dashboard.
Select the financial year and the return period, and click Search.
On the GSTR-3B tile, click Prepare Online. The portal may ask a few questions about the period first; answer them so only the relevant tables are shown.

Step 2: Check what the portal has already filled in

Much of GSTR-3B is now auto-populated:

Your outward supplies come from the GSTR-1 or IFF you filed for the period.
Your ITC comes from your GSTR-2B.

You can still edit most figures, but the portal will warn you when your entry differs a lot from the auto-filled value. Treat the auto-filled numbers as a starting point to check against your books, not as the final answer. You can also download the system-generated GSTR-3B summary (PDF) from the dashboard to compare.

Step 3: Go through the tables

You will mostly work in these tables:

Table 3.1, outward and reverse charge supplies: taxable sales, zero-rated supplies (exports and SEZ), nil-rated and exempt sales, inward supplies on which you pay tax under reverse charge, and non-GST supplies.
Table 3.1.1, supplies through e-commerce operators: only relevant if you sell certain services through platforms that pay GST on your behalf, or if you are such an operator.
Table 3.2, inter-state supplies: inter-state sales to unregistered buyers, composition dealers and UIN holders, shown state-wise. Many returns skip this and get notices later, so do not leave it blank if you sell to consumers in other states.
Table 4, eligible ITC: the credit you are claiming, the credit you must reverse, and the net ITC available. This is where most problems come from.
Table 5, exempt, nil-rated and non-GST inward supplies: purchases on which no GST credit is involved, such as purchases from composition dealers.
Table 5.1, interest and late fee: the portal calculates late fee for you. Interest for late payment is shown here too.

For example, take a Coimbatore textile trader who sells mostly within Tamil Nadu but has a few online orders from customers in Kerala and Karnataka. Those online sales go in Table 3.1 as taxable supplies, and also in Table 3.2 against Kerala and Karnataka, because the buyers are unregistered.

Once the figures match your books, click Save GSTR-3B.

Step 4: Pay the tax and offset liability

After saving, click Proceed to Payment. The portal shows:

the tax payable under IGST, CGST, SGST and cess,
the ITC available in your electronic credit ledger, and
the cash available in your electronic cash ledger.

The portal suggests how to use the credit to set off your liability, following the order the law requires (IGST credit first, then CGST and SGST). Check it, adjust if needed, and pay the balance in cash.

If the cash ledger does not have enough balance, click Create Challan. You can pay through net banking, debit or credit card, NEFT/RTGS from your bank, or over the counter at authorised banks for smaller amounts. Once the payment reflects in the cash ledger, come back and click Make Payment / Post Credit to Ledger.

Step 5: File with EVC or DSC

Tick the declaration and select the authorised signatory.
Click File GSTR-3B with EVC (an OTP comes to the signatory’s registered mobile and email) or File GSTR-3B with DSC (companies and LLPs must use DSC).
On success, an ARN (acknowledgement reference number) is generated and sent by SMS and email.

Download the filed return and the payment details for your records. Your auditor will ask for them at year end.

If you had no sales, no purchases and no tax to pay, you can file a nil GSTR-3B. Nil returns can also be filed by SMS from the registered mobile number.

Mistakes that lead to notices

Claiming ITC that is not in GSTR-2B. If a supplier has not filed, the credit will not appear in your GSTR-2B and you generally cannot claim it yet. Claiming more ITC than your GSTR-2B shows can trigger an automatic intimation from the portal.
Tax in GSTR-3B lower than in GSTR-1. If your GSTR-1 shows more tax than you paid in GSTR-3B, the system flags the difference and you will be asked to pay it or explain.
Forgetting reverse charge. Legal fees, GTA freight and some other services need tax paid in cash under reverse charge. ITC on that tax comes later, but the cash payment cannot be skipped.
Leaving Table 3.2 empty when you have inter-state sales to unregistered buyers.
Mixing up exempt and nil-rated sales, which affects how much ITC you must reverse.

What to do next

Before the next due date, sit down once and set up a simple monthly routine: post bills and purchases daily, download GSTR-2B as soon as it is available (usually around the 14th), match it with your purchase register, and only then open GSTR-3B. Most of the late-night stress goes away when the matching happens before the filing, not during it.

If your sales, purchases and GST data already live in one system, these figures come straight from your books. In Indeza VCloud, sales and purchase entries carry GST from the start, so the monthly summary for GSTR-3B is ready when you are. If you would like to see how that works for your business, you can book a demo.