GSTR-1 vs GSTR-3B: a monthly routine that keeps the two in agreement

Updated for FY 2026-27 (AY 2027-28).

Most first-time business owners file GSTR-1 and GSTR-3B without being sure why there are two of them, and discover the difference only when a notice arrives asking why the sales in one do not match the sales in the other. The two returns serve different purposes: one tells the department (and your customers) what you sold, the other tells the department what you are paying. This article explains the split, shows one month worked out in rupees with the journal entries, and ends with a checklist you can run every month in under an hour.

GSTR-1 is a statement of your outward supplies

GSTR-1 is a list of invoices, not a payment. For each month you report every tax invoice, credit note and debit note you issued: B2B invoices with the customer's GSTIN line by line, B2C sales in summary, exports, and any amendments to earlier months.

Two things follow from that.

First, GSTR-1 has no payment challan attached to it. Nothing leaves your bank account when you file it.

Second, GSTR-1 is the document your customer depends on. Whatever you report there flows into your customer's GSTR-2B, and that is where their input tax credit comes from. If you miss a B2B invoice in GSTR-1, your customer cannot take credit of the GST they have already paid you, and you will hear about it.

Due date: the 11th of the following month for monthly filers. For September sales, that is 11 October.

GSTR-3B is the summary return where tax is actually paid

GSTR-3B is a summary, not an invoice list. You report total outward taxable supplies and tax, total input tax credit available, any reverse-charge liability, and then pay the difference in cash.

The arithmetic is simple:

Output tax on sales − eligible input tax credit = cash payable through the electronic cash ledger.

Due date: the 20th of the following month for monthly filers. For September, that is 20 October.

The order matters. File GSTR-1 first, then GSTR-3B, because the sales figures in 3B should be the totals of the invoices you have just reported in GSTR-1. If 3B shows ₹8,40,000 of taxable sales and GSTR-1 shows ₹7,40,000, that ₹1,00,000 gap is the exact thing the system's comparison report flags.

The 2B rule: your credit is only as good as your supplier's filing

Input tax credit in GSTR-3B must be supported by GSTR-2B, the auto-generated statement of credit available to you. 2B is built from what your suppliers filed in their GSTR-1. The invoice on your desk is not enough on its own.

So each month, before filing 3B, open GSTR-2B and compare it with your purchase register. You will normally find three kinds of difference:

• In your books, not in 2B — the supplier has not filed, or filed with the wrong GSTIN. Do not claim it this month. Chase the supplier.
• In 2B, not in your books — a bill you have not recorded. Record it.
• In both, but amounts differ — usually a rate or a credit note. Fix the one that is wrong.

Keep the unclaimed amount in a separate ledger so you remember to claim it when the supplier catches up, instead of writing it off quietly.

One month worked out: Mehta Prints, Pune

September figures, all intra-state at 18%.

Sales: ₹8,40,000 taxable, GST ₹1,51,200 (CGST ₹75,600 + SGST ₹75,600). Invoice value ₹9,91,200.

Purchases and expenses: ₹5,00,000 taxable, GST ₹90,000 (CGST ₹45,000 + SGST ₹45,000).

On checking GSTR-2B, one paper supplier billed ₹1,00,000 + ₹18,000 GST and has not filed his GSTR-1. That ₹18,000 does not appear in 2B.

Eligible ITC = ₹90,000 − ₹18,000 = ₹72,000. Cash payable in 3B = ₹1,51,200 − ₹72,000 = ₹79,200.

The entries, assuming sales and purchases are recorded in the normal way:

Sales for the month

Purchases for the month

Moving the unmatched credit out of the claimable pool

Payment of September tax on 18 October

After these four entries, Output CGST, Output SGST, Input CGST and Input SGST are all nil, and the only GST balance left on the balance sheet is ₹18,000 sitting in "ITC pending in 2B". That single balance is your follow-up list. When the paper supplier files, the ₹18,000 appears in a later 2B, you claim it in that month's 3B and clear the ledger.

QRMP, and when the 11th and the 20th stop applying

If your aggregate turnover is up to ₹5 crore you may opt for the Quarterly Return Monthly Payment scheme. Returns go quarterly, but payment still happens every month through a challan for the first two months of the quarter. The point to grasp is that QRMP changes the filing rhythm, not the bookkeeping rhythm: you still have to close the month, reconcile the bank and check 2B, otherwise the quarter-end becomes three months of catching up in one week.

Registration itself is required once aggregate turnover crosses ₹40 lakh for goods or ₹20 lakh for services, with lower thresholds in special-category states. Many businesses register earlier anyway because their customers want the credit.

Your monthly GST checklist

Run this on fixed dates. Hour-long jobs become day-long ones only when they are late.

By the 3rd

1. Record every sales invoice for the previous month, including ones raised outside your software.
2. Record every purchase bill and expense bill, with GSTIN, invoice number and date as printed on the bill.
3. Reconcile all bank accounts and the petty cash book for the month, so no cash purchase is left out.

By the 7th 4. Check invoice number continuity — no gaps, no duplicates. Gaps invite questions. 5. Confirm credit notes are recorded against the original invoice and within time limits. 6. Tally your sales ledger to your outward tax ledger: tax at each rate should be the arithmetic you expect.

By the 10th 7. File GSTR-1, or prepare the data if you are on QRMP. 8. Send a statement to any customer who has queried credit, confirming their invoices are reported.

By the 14th 9. Download GSTR-2B and reconcile it line by line against the purchase register. 10. Move unmatched credit to the "ITC pending" ledger and e-mail the defaulting suppliers. 11. Check reverse-charge items — freight, legal fees, imports of service.

By the 18th 12. Compute output tax less eligible ITC, arrange the cash, pay the challan. 13. File GSTR-3B and save the acknowledgement in the month's folder. 14. Pass the payment entry so the GST ledgers close to nil, except pending ITC.

Separately, keep an eye on TDS while you are in the bills. The month-end bill review is the natural place to catch these liabilities, which apply once payments to a person in the financial year cross a threshold:

• 194J (professional fees): 10% once total payments cross ₹50,000.
• 194C (contractors): 1% or 2% once a single payment crosses ₹30,000 or total payments cross ₹1,00,000.
• 194I (rent): 10% once total payments cross ₹6,00,000.
• 194H (commission): 2% once total payments cross ₹20,000.

Where these numbers end up in your income-tax return

Your GST turnover is the starting point for the income-tax figure, though not identical to it — GST collected is not your income, and non-GST receipts still are.

Say Mehta Prints runs at the September rate all year, giving a taxable turnover of ₹1,00,80,000, with every rupee received by bank transfer or UPI. Under the presumptive taxation scheme of section 44AD, profit can be declared as a percentage of turnover. For receipts through digital modes, the rate is 6%, so the deemed profit is ₹6,04,800. (The turnover limit for this scheme is ₹3 crore, provided cash receipts are 5% or less of total turnover). Under the default new regime for FY 2026-27, the first ₹4,00,000 of income is nil-rated and the next ₹2,04,800 is taxed at 5%, giving ₹10,240. Since the total income is below ₹12 lakh, the rebate under section 87A brings the tax liability to nil. Advance tax under 44AD is payable in one instalment by 15 March, so this is worth computing in February rather than in July. Whether presumptive taxation suits you, given actual profits and partner salaries, is a conversation for your CA.

Doing this in FlipAccounts

Record sales and purchases on the Invoices and Bills screens with the customer or supplier GSTIN, and the GST summaries will build GSTR-1 and GSTR-3B figures from the same ledgers, so the two cannot drift apart. Use Bank reconciliation to import the month's statement from PDF, CSV or Excel and clear anything unrecorded before you look at 2B — see the reconciliation guide for the import steps. Keep a ledger named "ITC pending in 2B" in your chart of accounts and pass the reversal entry each month; it shows up on the balance sheet in the statements pack as your supplier follow-up list. Core accounting is free, with no card and no limits, and more detail on the GST side is in the free GST accounting software guide. CAs running this for several clients can switch between books from one login with a read-only auditor role, covered in the guide for CA firms.

What to do this week

1. Open last month's GSTR-1 and GSTR-3B side by side and check that taxable outward supplies agree; if they do not, list the invoices causing the gap.
2. Create an "ITC pending in 2B" ledger and move into it every rupee of credit you claimed but cannot see in 2B.
3. Put the 3rd, 10th, 14th and 18th in your calendar as recurring tasks, with the checklist above pasted into each one.

Frequently asked questions

Can I file GSTR-3B without filing GSTR-1 for the month?

The portal restricts 3B where GSTR-1 for the period is outstanding, and in any case it defeats the purpose — 3B is meant to summarise what 1 reports. File 1 first, by the 11th, then 3B by the 20th.

A supplier has not filed his GSTR-1, so the credit is missing from my 2B. Can I still claim it?

Credit must appear in GSTR-2B to be claimed, so take it in the month it appears rather than the month of the bill. Keep the amount in a separate ledger, send the supplier a written reminder, and hold payment of the GST portion if your contract allows it.

My sales figure in 3B is higher than GSTR-1 because of an advance received. Is that a mismatch?

Timing differences do happen, with advances, credit notes and amendments. The fix is to be able to explain the difference in a one-line reconciliation kept with the month's file, rather than to force the two numbers to agree. Where the treatment is unclear, check with your CA.

I am on QRMP. Do I still need to do this every month?

Yes, for the bookkeeping and the monthly payment challan. The filing is quarterly, but the bank reconciliation, 2B check and tax computation are still monthly tasks, and leaving them to quarter-end is how errors get built in.

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