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After your GST registration becomes effective, an online seller has two parallel jobs: report every period’s outward supplies in GSTR-1 and discharge the resulting tax liability through GSTR-3B. You must file the applicable returns even for a period with no sales. At the same time, every marketplace or direct-order invoice needs a controlled series, complete tax particulars, and a trail connecting orders, refunds, credit notes and (where applicable) e-invoice data.
The safest process is to start with the effective registration date, separate pre-registration and post-registration transactions, reconcile marketplace reports to your books, file GSTR-1 before GSTR-3B, and retain evidence of how the figures were calculated. Current portal instructions and state-specific notifications always take precedence over a standing calendar.
What should I do immediately after GST registration?
First confirm that the GSTIN shows as active on the GST Portal and record both the effective registration date and the certificate issue date. Those dates determine which supplies belong in your registered-period records and whether the revised-invoice facility can apply.
- Capture the registration dates. Save the registration certificate and an activation-status record. Mark the effective date in your accounting or order system.
- Split your transactions. Create separate lists for supplies before the effective date, supplies from the effective date through the certificate issue date, and supplies after the certificate was issued. Do not merge these periods merely because they appear in one marketplace settlement.
- Select a filing frequency if eligible. Decide whether monthly or quarterly filing fits your cash-flow and reporting workload. Record the choice and check that the portal reflects it.
- Set a compliance calendar. Add GSTR-1 and GSTR-3B tasks for every tax period. Recheck dates before filing because government notifications can alter due dates, especially for particular states or taxpayer categories.
- Lock your invoice controls. Use one consecutive invoice series for each GSTIN and financial year. Restrict editing rights and keep an audit trail for cancelled documents and credit or debit notes.
This setup prevents a common failure: filing a return from a marketplace payout statement without checking the underlying order date, place of supply, cancellations and tax treatment.
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Which GST returns does an online seller file?
Most normal and casual registered online sellers work with two recurring forms. They serve different purposes and should be prepared from the same reconciled sales ledger.
GSTR-1 records outward supplies
GSTR-1 is the monthly or quarterly statement of outward supplies for normal and casual registered taxpayers. It captures taxable sales and the prescribed details for supplies made through e-commerce operators, including the sections covering operator-collected tax under section 52 and supplies covered by section 9(5).
A nil period is still a filing period. The GST Portal’s GSTR-1 FAQ states that the form must be filed even when there is no business activity. “No orders” therefore means prepare and submit a nil GSTR-1 rather than leaving the period untouched.
GSTR-3B reports liability and payment
GSTR-3B is the summary return in which a normal or casual taxpayer reports tax liability and uses the available cash and input-tax-credit ledgers to settle it. For monthly filers, the usual due date is the 20th day of the month following the tax period. Quarterly filers generally receive a notified 22nd or 24th date, depending on the taxpayer’s state or category; verify the current notification on the portal.
Prepare the liability calculation from the same order, invoice, credit-note and refund data used for GSTR-1. A nil-sales period does not justify silently skipping the applicable return: determine whether a nil or liability return is required for that period and submit it through the portal.
How do I choose monthly or quarterly filing?
The choice changes how often you transmit data and pay tax, not the underlying invoice and record-keeping obligations.
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| Consideration | Monthly filing | Quarterly filing |
|---|---|---|
| Reporting rhythm | GSTR-1 and GSTR-3B work is performed each month. | Returns are submitted less frequently when the taxpayer is eligible and has selected the quarterly option; follow the portal’s associated procedures. |
| Cash-flow timing | Tax is generally reported and paid sooner after each month’s sales. | Cash remains with the business longer between filing events, but a larger period must be reconciled at once. |
| Operational workload | Smaller, more frequent reconciliations can expose order or tax-code errors earlier. | Fewer filing sessions require disciplined month-by-month ledgers so errors do not accumulate. |
| Dates | GSTR-3B is ordinarily due on the 20th of the following month, subject to notifications. | GSTR-3B commonly uses a notified 22nd or 24th date, depending on state or category. |
Use the frequency that your eligibility and current notification permit. Whichever option you select, close each month internally: reconcile orders, returns, cancellations, refunds, TCS and tax before the filing window arrives.
How should I create GST invoices for marketplace and direct sales?
An invoice is the source document for your return data. Create it at the time required by the GST rules for the supply, and make its number, tax calculation and order reference traceable from the customer order through settlement.
Required invoice fields
- Supplier’s legal name, address and GSTIN.
- A consecutive serial number unique for that GSTIN and financial year.
- Issue date.
- Recipient name and address, plus GSTIN or UIN when the recipient is registered or otherwise requires it.
- HSN code for goods or the Accounting Code for services.
- Description, quantity and unit of measure where relevant.
- Taxable value, applicable tax rate, tax amount and total invoice value.
- Place of supply and the intra-State or inter-State treatment where relevant.
- Links to credit or debit notes when an earlier invoice is adjusted.
- IRN and QR code when e-invoicing applies.
- Marketplace order, cancellation, refund and TCS references for platform transactions.
CBIC invoice rules require a consecutive serial number that is unique for the financial year. Do not reuse a number after deleting an invoice. If a document is cancelled, preserve the cancelled record and explain the next number in your invoice-control log.
Marketplace sales
Export the operator’s order, tax, cancellation, refund and TCS reports for each period. Map each sale to the appropriate e-commerce sections in GSTR-1 and retain the platform statements as reconciliation evidence. An operator that is required to collect tax under section 52 generally means the seller cannot rely on the small-supplier threshold exemption for those supplies.
Own-website sales
Direct orders still require the same invoice particulars, tax classification and outward-supply reporting. Where no e-commerce operator has a section 52 collection role, there may be no operator TCS statement to reconcile; that does not remove the seller’s obligation to determine place of supply, charge the correct tax and include the sale in the return.
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What is the difference between marketplace and own-website reporting?
The customer-facing channel changes the reconciliation evidence and possible TCS treatment, while the core GST invoice controls remain the same.
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| Workflow point | Marketplace order | Own-website order |
|---|---|---|
| Primary evidence | Seller invoice plus operator order, settlement, cancellation, refund and TCS files. | Seller invoice plus payment-gateway, shipping and order-system records. |
| Operator tax collection | Section 52 TCS may apply when the operator is required to collect it; section 9(5) supplies have their own reporting treatment. | No marketplace TCS file exists unless a separate operator arrangement creates that obligation. |
| GSTR-1 mapping | Use the e-commerce-operator sections and preserve the operator’s statement for reconciliation. | Report the outward supply in the applicable normal sections, based on the transaction’s tax and place-of-supply facts. |
| Refund handling | Match platform refund events to credit notes or other permitted adjustments and to the settlement report. | Match your store’s refund record to the invoice and adjustment document. |
Never treat a net marketplace payout as the taxable turnover figure without rebuilding the gross sale, tax, commission, refunds and TCS components.
When does e-invoicing change my workflow?
When e-invoicing applies to your business and transaction type, the Invoice Registration Portal (IRP) receives the invoice data, generates an Invoice Reference Number (IRN), and returns the signed information and QR code. GST systems can then use that data for return preparation, reducing duplicate entry.
- Generate the invoice in your accounting or approved billing system with the required GST fields.
- Transmit the data to the IRP through the approved integration or upload method.
- Capture the IRN and QR code on the invoice and store the returned signed data.
- Download or import the e-invoice data into your GSTR-1 preparation workflow.
- Review the imported records against orders, tax calculations, cancellations, credit notes and marketplace statements.
- Correct errors or make permitted amendments before filing. Do not assume that an IRN means every return field is already correct.
E-invoice transmission and return filing are connected but not interchangeable. Your responsibility remains to check the imported population, identify omissions or duplicates, and retain the IRP response with the invoice record.
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Manual creation can be a practical fallback for a small seller, but it does not bypass electronic filing or e-invoice obligations when those rules apply.
| Issue | Manual invoice process | E-invoice process |
|---|---|---|
| Creation | Enter the prescribed fields in billing software or a controlled paper form. | Generate structured data and transmit it to the IRP through an approved route. |
| Number control | Maintain a consecutive series and a register for issued, cancelled and adjusted documents. | Maintain the same series discipline while also storing the IRN and returned document. |
| Return preparation | Enter or upload invoice data into the return workflow after reconciliation. | Import IRP data, then review and amend the return population before filing. |
| Operational risk | Transcription mistakes, duplicate numbers and lost paper are the main risks. | Interface failures, rejected payloads, incorrect master data and unreviewed imports are the main risks. |
| Legal boundary | Useful for permitted transactions or continuity, but cannot replace required e-invoicing. | Required only where the current e-invoice rules cover the taxpayer and supply. |
Using a GST invoice book as a backup
A numbered GST invoice book can preserve continuity during a short system or connectivity outage, provided each document contains the prescribed particulars and is entered into your electronic records afterward. Treat it as a controlled backup: issue numbers from the same series, record the reason for manual issuance, and reconcile every handwritten invoice to the later return and, where required, e-invoice process.
What should I reconcile before filing GSTR-1?
Build a period-end worksheet that explains every difference between your order systems, invoices, operator reports and the return draft.
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- Start with the complete order export, including cancelled orders and orders dispatched in a different period.
- Match each order to an invoice number, GSTIN or customer status, HSN/SAC, tax rate, taxable value and place of supply.
- Separate credit notes, debit notes, refunds and replacement shipments from original sales.
- For marketplace orders, tie gross sales to the operator’s settlement, commission, TCS and refund files rather than using only the deposited amount.
- For e-invoices, compare the IRP response and imported GSTR-1 data with your source ledger; investigate rejected, duplicated or missing IRNs.
- Document any amendment with the original invoice number, reason and period in which the adjustment is reported.
Save the worksheet and source exports with the filing acknowledgement. This gives you a repeatable explanation if a later review finds that a marketplace total, refund or tax amount changed.
How do I file GSTR-1 and GSTR-3B in the right order?
File GSTR-1 after the outward-supply data is reconciled, then use the resulting liability figures to complete GSTR-3B and payment.
- Close the period internally and freeze the invoice, credit-note and refund population.
- Open GSTR-1 on the GST Portal and select the correct tax period and filing frequency.
- Enter or import outward supplies, including the prescribed e-commerce-operator sections and any e-invoice data.
- Run the portal’s validation, inspect warnings and compare the draft totals to your worksheet.
- Submit and file GSTR-1, retaining the acknowledgement and filed data.
- Prepare GSTR-3B from the reconciled liability and eligible ledger balances, not from the marketplace payout alone.
- Pay the amount due from the cash ledger and use eligible input tax credit according to the portal’s available balances and rules.
- Save challans, ledger screenshots or downloads, return acknowledgements and the reconciliation file together.
If a portal figure differs from your books, stop and identify the source—an omitted order, duplicate invoice, late refund, incorrect place of supply or imported e-invoice error—before filing a number you cannot support.
Independent reader supportYour contribution helps us test, update, and keep practical guides available for everyone.What if I issued invoices between the effective date and certificate date?
CBIC rules permit revised tax invoices for supplies made from the effective registration date until the certificate issue date, subject to the conditions in the applicable rule. Preserve the original transaction trail and use the permitted revised-invoice process rather than silently replacing documents.
- Identify supplies whose tax point falls within that date window.
- Retain the original invoice, order, delivery and payment evidence.
- Prepare the revised tax invoice with the required GST particulars and a clear reference to the original document.
- Ensure the revised document uses the controlled series and is reflected consistently in your sales ledger, GSTR-1 and GSTR-3B.
Do not extend this treatment to supplies before the effective registration date without checking the specific legal provision that applies to your facts.
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Electronic records are efficient for imports, sorting and reconciliation; a paper backup can keep invoicing moving during a device, software or connectivity interruption. The strongest small-seller process uses electronic records as the primary ledger and a controlled paper option only for continuity.
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| Control | Electronic record | Paper backup |
|---|---|---|
| Best use | Routine order capture, return preparation, IRP imports and reconciliation. | Temporary invoicing when the primary system is unavailable. |
| Numbering | System-enforced sequence with access controls. | Pre-numbered or manually controlled sequence tied to the GSTIN and financial year. |
| Recovery requirement | Regular exports or backups and a documented restoration process. | Prompt entry into the electronic ledger after the disruption ends. |
| Risk to monitor | Corrupt imports, duplicate records and unreviewed automated data. | Illegible fields, missing copies, skipped numbers and delayed posting. |
Whichever medium you use, retain the invoice, adjustment document, order reference and filing evidence as one traceable record.
What are the most common online-seller GST mistakes?
- Skipping a nil GSTR-1: no sales is not the same as no filing obligation.
- Using payout totals: settlements may be net of commission, TCS, refunds and other adjustments.
- Reusing invoice numbers: a serial must remain unique for the financial year.
- Ignoring place of supply: the same product can have different tax treatment depending on the transaction facts.
- Assuming IRP data is final: imported e-invoice records still need review and permitted amendments.
- Mixing registration periods: effective-date transactions and earlier sales need separate analysis.
- Failing to retain source reports: without order and operator exports, a return total cannot be reconstructed reliably.
A monthly internal close, even for a quarterly filer, is the simplest way to catch these errors while the order and refund data are still available.
Frequently Asked Questions
Can I use the same invoice number series for two GSTINs?
Use a separate controlled series for each GSTIN and financial year. The invoice serial requirement is tied to the registered supplier, so a number used for one GSTIN should not be reused for another’s documents.
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Keep the original invoice and the platform’s refund event together, issue or record the permitted adjustment document with a reference to that invoice, and report the adjustment in the period allowed by the applicable GST procedure. Reconcile the change to the operator statement rather than altering the original sales record invisibly.
Is a paper GST invoice book enough for return compliance?
It can provide a temporary or manual backup, but it does not replace electronic return filing or e-invoicing where those requirements apply. Post each paper invoice into your electronic ledger and preserve the number sequence and supporting order evidence.
How can I tell whether my GSTR-1 data is complete before submitting it?
Compare the draft return with your frozen order ledger, invoice register, credit and debit notes, refund list, marketplace TCS file and any IRP import. Investigate every difference and keep the reconciliation worksheet with the filed acknowledgement.
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