GST Return Filing Handbook 2026: Complete Compliance Calendar, ITC Reconciliation, and Penalty Schedule

TL;DR

Every regular GST taxpayer in India files GSTR-1 by the 11th of the following month and GSTR-3B by the 20th — capturing outward supplies and the tax self-assessment respectively. The annual GSTR-9 is due 31 December of the following financial year, and GSTR-9C reconciliation is required for turnover above ₹5 crore. Late fee under Section 47 runs ₹50/day (₹20/day for NIL returns) capped at ₹10,000 per Act per period; interest under Section 50 runs 18% per annum on unpaid tax. The four returns are not redundant — GSTR-1 feeds your customers’ ITC claims, GSTR-3B triggers your tax payment, GSTR-9 reconciles the year against your audited books, and GSTR-9C bridges the gap with the audit. This handbook walks through each return, each deadline, each reconciliation workflow, and the late fee and penalty schedule for FY 2025-26 onwards.

The 2026 Filing Calendar

The GST return filing calendar for a regular taxpayer (non-QRMP) follows a fixed monthly cycle plus the annual return and (for turnover above ₹5 crore) the reconciliation statement.

Monthly cycle (12 times per year):

• Day 1-10 of month M+1: Prepare GSTR-1 for month M
• Day 11 of month M+1: GSTR-1 due (13th for QRMP)
• Day 12-13: GSTR-2B auto-generated from suppliers’ GSTR-1 filings
• Day 14-19 of month M+1: Prepare GSTR-3B for month M
• Day 20 of month M+1: GSTR-3B due (22nd-24th for QRMP)

Annual cycle (1 time per year):

• 31 December of FY+1: GSTR-9 (annual return) due for the FY that just ended on 31 March
• 31 December of FY+1: GSTR-9C (reconciliation statement) due if aggregate turnover during the FY exceeded ₹5 crore

Quarterly cycle (composition scheme only):

• 18th of month following the quarter: CMP-08 due for the quarter

Special-period returns:

• GSTR-5 (non-resident): 20th of the month following the tax period
• GSTR-5A (OIDAR): 20th of the month following the tax period
• GSTR-6 (input service distributor): 13th of the following month
• GSTR-7 (TDS deductor): 10th of the following month
• GSTR-8 (TCS collector): 10th of the following month

The due dates are fixed by Section 37 (GSTR-1), Section 39 (GSTR-3B), and Section 44 (GSTR-9), read with the 22nd GST Council meeting notification. There is no general relaxation for weekends or holidays — late fee accrues for every day of delay including non-working days.

What Each Return Captures

GSTR-1 — outward supplies register. Filed by every regular taxpayer. Captures every invoice issued during the month: B2B with customer GSTIN, B2C by state and rate, exports with shipping bill, advances received, credit notes and debit notes. HSN-wise summary in Table 12. Once filed, the data flows into every supplier’s GSTR-2B within 24-48 hours, which is when your customers can claim ITC on what they bought from you.

GSTR-3B — summary self-assessment. The only return that triggers tax payment. Captures output tax on outward supplies, eligible ITC auto-populated from GSTR-2B, ITC reversed under Rule 42/43, ineligible ITC under Section 17(5), and interest under Section 50 + late fee under Section 47. The net cash outflow equals output tax minus eligible ITC, plus interest and late fee, all paid via Electronic Cash Ledger.

GSTR-9 — annual reconciliation. A single-document reconciliation between the cumulative GSTR-1 and GSTR-3B filed during the year and the audited annual accounts. Tables 8 and 9 of GSTR-9 capture the reversals and ITC claimed during the year. Differences above ₹1 lakh per head attract notice under Section 73. For FY 2024-25, GSTR-9 is due 31 December 2025.

GSTR-9C — reconciliation statement. Required for turnover above ₹5 crore. Self-certified by the taxpayer (no CA certification required since FY 2022-23 amendment, unless turnover exceeds ₹10 crore). Reconciles GSTR-9 with the audited financial statements — Table 5 captures the reconciliations.

CMP-08 — composition quarterly statement. Filed by composition scheme taxpayers instead of monthly GSTR-1 / GSTR-3B. Captures turnover, tax payable at composition rate (1% for traders, 5% for restaurants), and any input used for ineligible purposes. Due 18th of the month following each quarter.

ITC Reconciliation Workflow

The most failure-prone part of monthly GST filing is the ITC reconciliation between GSTR-2B (auto-generated) and the taxpayer’s purchase register. The workflow we use at FinTax24 for our 12,000+ monthly filings:

Day 1-3 of month M+1: data extraction. Pull all purchase invoices entered in Tally / Zoho Books / QuickBooks / Busy during month M. The accounting system holds the invoices even if the supplier hasn’t filed GSTR-1 yet — so the register is the source of truth for “what we bought”.

Day 4-7: GSTR-2B arrival. On day 13 of month M+1, the GSTN generates GSTR-2B for month M from suppliers’ GSTR-1 filings. We download the GSTR-2B JSON from the GST portal and compare it line-by-line against the purchase register.

Day 8-10: reconciliation and supplier follow-up. For each purchase invoice in the register that does NOT appear in GSTR-2B, we:

• Verify the supplier’s GSTIN is correct
• Check if the supplier has filed GSTR-1 for that period (most missing invoices are suppliers who haven’t filed yet)
• Send a formal email reminder to the supplier with the invoice number and amount
• Flag invoices from suppliers who have stopped filing (potential ITC blockage under Section 16(2))

The reconciliation typically recovers 5-15% of total ITC that would otherwise be lost. In one recent quarter, we recovered ₹14 lakh of ITC across 47 client filings by systematically chasing 200+ suppliers.

Day 11: GSTR-1 filing. Output side filed.

Day 12-18: GSTR-3B preparation. Open GSTR-2B in the GST portal, apply ITC reversals under Rule 42 (for input services used partly for exempt supplies) and Rule 43 (for capital goods used partly for exempt supplies), add ineligible ITC under Section 17(5) — motor vehicles, food and beverages, club membership, cosmetics, health and life insurance (with exceptions). Compute net tax. Generate the PMT-06 challan for the Electronic Cash Ledger.

Day 19-20: GSTR-3B filing. Top up the cash ledger via NEFT/RTGS one day before. Submit. ARN recorded.

Day 21-30: post-filing review. Respond to any officer queries under Section 61 (scrutiny), manage refund claims if eligible, update books with the actual cash outflow, prepare ITC reversals for non-payment to suppliers within 180 days (Section 16(2)(b)).

Reverse Charge Treatment

Reverse charge under Section 9(4) shifts the GST payment obligation from the supplier to the recipient. The recipient must include the supply in their GSTR-3B Table 3.1(d) and pay the tax via cash ledger. The most common reverse-charge scenarios:

• Legal services from an advocate (Section 9(3) — irrespective of aggregate turnover)
• Renting from an unregistered landlord for residential use (above ₹20,000/month per individual agreement)
• Goods transport agency (GTA) services from an unregistered transporter
• Services from a director or a related person (other than salary) where the supplier is not registered
• Import of services from a person outside India (Section 9(4) read with Section 13 — time of supply rules)

For each reverse-charge supply, the recipient:

• Self-invoices the supply in their books (Section 31(3)(f))
• Includes the value in GSTR-3B Table 3.1(d)
• Pays the tax in cash (no ITC available for cash payment under reverse charge — the recipient does, however, get ITC on the reverse-charge payment if the supply is for business use)
• Files GSTR-1 with the reverse-charge details in Table 7C

The reverse-charge workflow is integrated into the monthly GSTR-3B cycle — there is no separate return for it.

Late Fee and Interest Schedule

For FY 2025-26 (assuming no further amendment):

Return	Late fee per day	Cap (per Act per period)	Interest under Section 50
GSTR-1	₹50 (₹25 CGST + ₹25 SGST)	None specified (no cap)	n/a (no tax payment)
GSTR-3B	₹50 (₹25 CGST + ₹25 SGST)	₹10,000 per Act (₹20,000 total)	18% per annum on unpaid tax
GSTR-3B NIL	₹20 (₹10 CGST + ₹10 SGST)	₹5,000 per Act (₹10,000 total)	n/a (no tax)
GSTR-9	₹100 (₹50 CGST + ₹50 SGST)	0.25% of aggregate turnover	n/a (reconciliation only)
GSTR-9C	₹50 per Act	₹10,000 per Act	n/a
CMP-08	₹50 (composition)	₹5,000 per Act	18% per annum

The late fee cap for GSTR-3B of ₹10,000 per Act (₹20,000 combined CGST + SGST for intra-State filers) was set by Notification 7/2023-CT. Before this notification, the cap was ₹5,000 per Act — so older returns (filed before July 2023) have a lower cap.

Interest under Section 50 starts accruing from the day immediately after the due date of payment till the day of actual cash ledger debit. For GSTR-3B unpaid tax of ₹10 lakh for 90 days, interest = ₹10,00,000 × 18% × 90/365 = ₹44,383.

Section 122 penalty (up to ₹10,000 per offence or amount of tax evaded, whichever is higher) applies only after a Show Cause Notice under Section 73 or 74, personal hearing, and order. For routine monthly late filings, the late fee + interest is the standard exposure.

E-Invoicing and E-Way Bill

Two complementary electronic systems work alongside GSTR-1:

E-invoicing under Notification 13/2020-CT (amended) requires businesses with aggregate turnover above ₹5 crore to generate an IRN (Invoice Reference Number) and 64-character QR code through the GSTN’s e-invoice portal for every B2B invoice. The threshold dropped from ₹10 crore (1 April 2021) to ₹5 crore (1 April 2023) and may drop further in future. Below threshold, e-invoicing is voluntary.

E-invoice data flows automatically into GSTR-1, eliminating the need to manually upload invoices — the e-invoice portal pushes the data, and the GSTR-1 form auto-populates from it. For businesses above the threshold, this is a significant time-saving.

E-way bill under Section 68 read with Rule 138 is required for every inter-State movement of goods of value exceeding ₹50,000. For intra-State movement, the threshold varies by State (₹50,000 in most, ₹15,000 in a few smaller States). The e-way bill is generated on the ewaybillgst.gov.in portal and carries a unique 12-digit number. Validity depends on distance: 100 km = 1 day for normal goods, 75 km = 1 day for ODC (over-dimensional cargo). Extension possible before expiry.

E-way bill is independent of GSTR-1 — both must be generated, and the e-way bill number is often referenced in the corresponding GSTR-1 invoice for matching. Inconsistencies (e-way bill issued but no invoice in GSTR-1, or invoice in GSTR-1 but no e-way bill) trigger department notices.

The Seven Most Common Filing Errors

Based on FinTax24’s review of 12,000+ monthly returns:

1. HSN code mismatch. Using 4-digit HSN when 6-digit is required (or vice versa) for the taxpayer’s turnover band. Since 1 April 2021, 6-digit HSN is mandatory for turnover above ₹5 crore.
2. Tax rate-versus-HSN mismatch. Charging 18% on a 12% HSN code (or 28% on an 18% code). The 12% slab was discontinued in the 2025-26 rationalisation — many taxpayers haven’t updated their master data.
3. Inter-State vs intra-State confusion. Treating a supply as intra-State when the buyer is in a different State, or vice versa. Causes IGST vs CGST + SGST mismatches.
4. ITC claimed on blocked items. Section 17(5) blocks ITC on motor vehicles, food, club, cosmetics, health insurance (with industry-specific exceptions).
5. Credit note timing. Issuing credit notes in a different period than the original invoice, causing GSTR-1 mismatch.
6. Advance receipt treatment. Failing to declare advances against future supply (taxable at receipt under Section 12 for goods, Section 13 for services).
7. Late GSTR-2B reconciliation. Most practitioners download GSTR-2B but fail to reconcile it against the purchase register. The unreconciled invoices are then claimed or missed in subsequent months, creating cumulative errors.

How FinTax24 Handles Monthly Filing

Our monthly process for a typical mid-size client (turnover ₹5-50 crore):

• Day 1-3: Data extraction from accounting system + manual entry collation
• Day 4-7: GSTR-2B reconciliation + supplier follow-up emails (recoveries ~5-15% of ITC)
• Day 8-10: GSTR-1 preparation + filing on day 11
• Day 12-18: GSTR-3B preparation + GSTR-2B integration + reversals + cash ledger top-up
• Day 19-20: GSTR-3B filing
• Day 21-30: Post-filing review, refund management, supplier communication

For clients above the e-invoice threshold, the IRN generation is integrated into the invoice creation in the accounting system, and GSTR-1 auto-populates from the IRN data.

Frequently Asked Questions

What if I miss the GSTR-1 due date but file GSTR-3B on time?

You pay Section 47 late fee for the days GSTR-1 is delayed (₹50/day, no cap on GSTR-1 — but in practice the practical cap applies via Section 73 proceedings). GSTR-3B can be filed independently — there is no linkage in the GST portal that blocks GSTR-3B for late GSTR-1. However, the late GSTR-1 means your suppliers’ GSTR-2B is missing your invoices, which means their ITC is wrong, which means their GSTR-3B may be underpaid or over-claimed. The downstream impact is bigger than the late fee itself.

Can I revise a filed GSTR-1 or GSTR-3B?

GSTR-1 can be revised before the GSTR-3B due date (20th of the following month) using the Amendment Table 9 / 10. GSTR-3B cannot be revised — errors must be corrected in the next month’s return (Table 4 for ITC, Table 5/6 for reversals). For substantive errors, an Annual GSTR-9 revision is possible within the window allowed under Section 44 (currently 31 December of the following FY for FY 2024-25).

What happens if I claim ITC on an invoice whose supplier hasn’t filed GSTR-1?

The auto-populated GSTR-2B excludes the supplier’s invoice. If you claim ITC on an invoice not in GSTR-2B, the credit may be reversed under Section 16(2)(c) on audit. The proper workflow: chase the supplier to file GSTR-1 first, then claim ITC the following month when the invoice appears in your GSTR-2B.

Can I claim ITC on a credit note issued to me?

Yes — the supplier’s credit note appears in your GSTR-2B Table 3 (negative entry), which reduces your eligible ITC the following month. The timing aligns with the supplier’s filing of GSTR-1 with the credit note.

What is the difference between Section 73 and Section 74?

Section 73 covers non-fraud cases — regular late filing, short-payment, excess ITC claim — with the standard penalty of 10% of the tax short-paid (Section 73(11)). Section 74 covers fraud cases — wilful mis-statement, suppression of facts, issuance of invoices without underlying supply — with the higher penalty of 100% of the tax short-paid (Section 74(1)). The standard late filing + interest exposure under Section 47 + 50 falls under Section 73, not Section 74.

How do I handle e-invoice errors after filing?

E-invoice errors (wrong GSTIN, wrong amount, wrong HSN) can be corrected by cancelling the original IRN (within 24 hours of generation, before GSTR-1 filing) and issuing a new invoice with a fresh IRN. After GSTR-1 is filed, the only way to correct is via the Amendment Table 9 of the next GSTR-1, or via GSTR-9 reconciliation at year-end.

Can I use the QRMP scheme mid-year?

The QRMP (Quarterly Return Monthly Payment) scheme requires an opt-in declaration in Form GST REG-01 (or amendment via GST REG-02) at the start of a quarter. Once opted in, you cannot switch back to monthly filing for that quarter. The scheme applies to small taxpayers with turnover up to ₹5 crore.

What is GSTR-2B and how is it different from GSTR-2A?

GSTR-2A is a dynamic statement that updates as your suppliers file GSTR-1 throughout the month. GSTR-2B is a static statement generated on the 13th of the following month, locking in the supplier data for ITC claims. You should claim ITC based on GSTR-2B, not GSTR-2A — because GSTR-2B is the version the system uses for GSTR-3B auto-population.

How to Get Started

For first-time filers, the GST Registration service sets up your GSTIN in 3-5 working days. For ongoing monthly filing, the GST Return Filing service handles both GSTR-1 and GSTR-3B with full ITC reconciliation, supplier follow-up, and an annual GSTR-9 included.

For e-invoice enabled businesses, the workflow integrates with Tally / Zoho Books / QuickBooks to push IRN generation directly from your accounting system. For e-way bill, the FinTax24 portal integration pushes e-way bill generation alongside your GSTR-1 filing so the two are always consistent.

Talk to our indirect-tax desk for a free 30-minute consultation on which return types apply to your business, what your ITC recovery opportunity is, and the typical compliance cost for your turnover band.