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After GST registration, an online seller has two recurring jobs: issue compliant invoices and report every taxable transaction in the correct return. That means filing GSTR-1 for outward supplies, filing GSTR-3B to declare and pay the liability, reconciling marketplace orders and TCS, and submitting nil returns when a period has no activity. Your first control is the effective date on the registration certificate: transactions from that date must be separated from earlier sales, even if the certificate was issued later.
The workflow below covers marketplace and own-website sales, monthly and quarterly filing, manual and e-invoice creation, refunds, cancellations, and invoices issued between the effective registration date and certificate issue date. GST notifications and portal functionality can change, so verify the current dates and applicability shown for your GSTIN before each filing.
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What must an online seller do after GST registration?
Set up an invoice series, map each order to the correct place-of-supply and tax treatment, file GSTR-1 and GSTR-3B for every tax period, and keep a reconciliation trail from order data to tax payment. Registration does not make marketplace reports a substitute for your returns; those reports are source records that must agree with what you declare.
Start with the effective registration date
- Download the registration certificate and note the effective registration date, GSTIN, and the date the certificate was issued.
- Split sales, advances, cancellations, refunds, and credit notes into transactions before the effective date and transactions on or after it.
- Use the permitted revised-invoice procedure for supplies made from the effective date until the certificate issue date, keeping the original order and payment trail.
Do not treat the certificate issue date as the only date that matters. The effective date determines which supplies fall into the registered period, subject to the conditions in the applicable invoice rules.
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- Consecutively Numbered: Enlarged red 6-digit numbers in the upper right corner of each invoice receipt book help you quickly navigate through your orders.
- Wraparound Divider Flap: A thick folded cardboard divider is integrated into the back of each invoice book for use between each two-part sales order to prevent the written content from rubbing off on subsequent copies of the invoice, resulting in wasted invoices.
- 2 Packs/50 Sets (100 Sets Total): Each invoice book provides 50 sequentially numbered carbonless sets of 2 invoice books for long-term use.
- Customizable Space: Each invoice book for small business has space at the top to add a company seal or sticker.
Choose a filing frequency you can operate reliably
Eligible taxpayers generally choose monthly or quarterly filing. The choice changes how often data and cash are reported; it does not remove the need to capture every order, return, or adjustment as it happens.
| Choice | Operational pattern | What to watch |
|---|---|---|
| Monthly | Prepare and file GSTR-1 and GSTR-3B for each month. | More frequent reconciliations and payments, but smaller periods to investigate when an order or refund is missing. For monthly GSTR-3B filers, the usual due date is the 20th of the following month, subject to notifications. |
| Quarterly | Report eligible periods quarterly under the applicable scheme and portal workflow. | Fewer filing events, but a larger backlog of marketplace reports and adjustments. GSTR-3B dates are notified as the 22nd or 24th for relevant quarterly groups; confirm the date applicable to your state and scheme. |
Put both return types on a calendar as soon as the GSTIN is active. Check the portal and current state-specific notifications before filing because due dates, holidays, and scheme rules can be changed.
Which GST returns does an online seller file?
For a normal or casual registered taxpayer, GSTR-1 records outward supplies and GSTR-3B records the tax liability and payment. They serve different purposes and must agree after accounting for eligible adjustments.
What goes into GSTR-1?
GSTR-1 is the monthly or quarterly statement of outward supplies. Include taxable sales, applicable exports or other reportable categories, credit and debit notes, and supplies made through e-commerce operators in the sections provided by the portal. Marketplace transactions can involve section 52 tax collected at source (TCS) and supplies covered by section 9(5), so do not place every platform order in a generic sales bucket.
File GSTR-1 even when there was no business activity in the period. A nil GSTR-1 is still a filing; inactivity is not a reason to leave the period open.
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- CONSECUTIVELY NUMBERED: Large 6-digit numbers in the upper right hand corner help you thumb through orders quickly
What goes into GSTR-3B?
GSTR-3B is the summary return in which normal and casual taxpayers declare liability and discharge it using the available cash and input-tax-credit ledgers. For monthly filers, the portal FAQ states the usual due date as the 20th day of the following month. For eligible quarterly filers, notified due dates are commonly the 22nd or 24th, depending on the applicable state or group.
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What if there were no sales?
Submit a nil GSTR-1 and the applicable nil or liability return for the period when there were no reportable supplies. Confirm that there were also no credit notes, advances, reverse-charge items, or other entries requiring disclosure; “no orders” alone does not prove that every return field is empty.
How should I create GST invoices for marketplace and own-website orders?
Use one controlled invoice process for all channels, then add marketplace-specific references and reporting fields. An invoice should allow a reviewer to trace the tax calculation from the seller and buyer details to the underlying order.
Build a compliant invoice series
- Create a consecutive serial-number series for each GSTIN and financial year. Do not reuse a number or create duplicates across spreadsheets, stores, or staff members.
- Record the legal supplier name, address, and GSTIN exactly as registered.
- Capture the issue date and, when applicable, the recipient’s name, address, GSTIN or UIN, and registration status.
- Enter the HSN code for goods or the Accounting Code for services, with a clear description.
- For goods, record quantity and unit where relevant. Record taxable value, tax rate, tax amount, and the total invoice value.
- Apply the correct inter-State or intra-State treatment and record place-of-supply information where required.
- Link every credit or debit note to the original invoice or transaction and state the reason for the adjustment.
- For a platform order, add the marketplace order ID and retain references to cancellation, refund, commission, and TCS reports.
CBIC invoice rules require a consecutive serial number unique for the financial year, along with prescribed supplier, recipient, supply, and tax particulars. A marketplace-generated packing slip or payment receipt is not automatically a GST tax invoice unless it contains the required information and is issued by the correct supplier.
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- WRAP-AROUND COVER: Fold the back cover between sets to keep invoices neat and legible
- CONSECUTIVELY NUMBERED: Large 6-digit numbers help you thumb through invoices quickly
- STOCK UP: Each book includes 50 white/canary sets; order several to keep your favorite forms on hand
Marketplace versus own-website sales
| Issue | Marketplace order | Own-website order |
|---|---|---|
| Operator reporting | Map supplies to the e-commerce-operator sections in GSTR-1, including relevant section 52 TCS and section 9(5) cases. | No operator TCS mapping for the seller’s own checkout, but normal outward-supply reporting still applies. |
| Threshold question | A seller using an operator that must collect TCS generally cannot rely on the ordinary registration-threshold exemption. | Threshold and registration treatment depend on the seller’s facts and current law. |
| Evidence to retain | Order, settlement, cancellation, refund, commission, tax and TCS reports, reconciled to invoices. | Order, payment-gateway, shipping, cancellation and refund records reconciled to invoices. |
| Customer data | Use the customer GSTIN and address supplied for the order where the customer is registered; resolve invalid data before filing. | Collect and validate the same details through the seller’s checkout and support process. |
The operator’s TCS statement does not replace your outward-supply entry. It is a reconciliation input that helps explain why the marketplace settlement differs from the invoice value.
How do e-invoices flow into GSTR-1?
Where e-invoicing applies to your business, invoice data is transmitted to the Invoice Registration Portal (IRP). The IRP issues an Invoice Registration Number (IRN) and QR code, and the information is transferred to GST systems so it can flow into return preparation.
Use this e-invoice workflow
- Confirm that your GSTIN, turnover category, transaction type, and date fall within the current e-invoicing mandate. The mandate and thresholds are notification-driven.
- Generate the invoice in your accounting or approved billing system with the same supplier, buyer, value, tax, and place-of-supply fields used for the sale.
- Transmit the required data to the IRP, directly or through an approved integration.
- Capture the returned IRN and QR code and place them on the invoice supplied to the recipient.
- Download the IRP and GST-system data into your return working file.
- Compare imported records with orders, cancellations, credit notes, and marketplace settlements. Correct errors through the permitted amendment or cancellation process before filing.
Automation reduces duplicate typing; it does not remove review responsibility. An incorrect buyer GSTIN, tax rate, place of supply, or value can flow into a return unless you identify it during reconciliation.
Manual invoices and a paper backup
If e-invoicing is not applicable, a compliant electronic invoice or a controlled manual process can be used. A GST invoice book can provide continuity during a device, connectivity, or system outage, but every handwritten number must later be entered into the same accounting and return records. It cannot replace portal filing, an IRN where required, or the prescribed tax particulars.
| Method | Strength | Risk and control |
|---|---|---|
| Electronic invoice system | Searchable records, automatic numbering controls, and easier order reconciliation. | Integration or mapping errors; lock the series and review exception reports. |
| Manual GST invoice backup | Can keep dispatches documented during a short operational disruption. | Duplicate numbers or omissions; reserve a controlled range and enter each invoice into the main ledger promptly. |
How do I reconcile marketplace sales before filing?
Reconcile at transaction level first, then aggregate for the return. Settlement totals alone are not enough because platforms may net commissions, TCS, refunds, shipping charges, and cancellations before paying you.
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Collect the source reports
- Order and tax-invoice export, including order ID, invoice number, date, taxable value, tax rate, and tax amount.
- Cancellation, return, refund, replacement, and credit-note reports.
- Settlement and fee reports showing deductions and payout dates.
- TCS reports and any operator statement needed to match section 52 entries.
- Own-website payment, shipping, and refund exports for sales outside the marketplace.
Run the reconciliation
- Match each order ID to an invoice number and confirm that the invoice series has no gaps that are unexplained.
- Separate the sale date from the settlement date; use the correct tax-period rule rather than the bank-credit date alone.
- Match cancellations and refunds to the original invoice and create the required credit-note or adjustment trail.
- Compare the platform’s taxable value and tax with your ledger, then investigate differences caused by fees, discounts, shipping, or tax-inclusive pricing.
- Match reported TCS to the operator statement and preserve the statement with your working papers.
- Aggregate the reconciled data into the applicable GSTR-1 tables and carry the resulting liability into GSTR-3B.
Keep a dated reconciliation file showing the opening order export, adjustments, final return totals, and payment reference. That file makes a later correction explainable without rebuilding the period from a settlement bank statement.
Independent reader supportYour contribution helps us test, update, and keep practical guides available for everyone.What should I do about invoices issued before the GST certificate arrived?
First identify whether the supply occurred on or after the effective registration date. For supplies in that interval, CBIC rules permit revised tax invoices from the effective registration date until the certificate issue date, subject to the conditions in the rule.
- List each affected original invoice, order, customer, taxable value, tax, and supply date.
- Check that the supply falls within the effective-date-to-certificate window and that the customer details support the revised document.
- Issue the revised tax invoice using the controlled series and link it to the original transaction record.
- Report the revised supply in the correct GSTR-1 period and include its liability in GSTR-3B.
- Retain both the original document and revised invoice so the sequence is auditable.
Transactions completed before the effective registration date require separate treatment; do not backdate a GST invoice merely because the certificate arrived later.
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What filing-day checks prevent common errors?
- GSTIN status: Confirm the registration is active and that the return period matches the effective date.
- Numbering: Search all sales channels for duplicate invoice numbers or unexplained gaps.
- Tax treatment: Check place of supply, inter-State versus intra-State tax, HSN or service code, and rate.
- Adjustments: Tie every cancellation, return, refund, credit note, and debit note to its source invoice.
- Marketplace data: Match operator TCS and platform totals to order-level records.
- E-invoice data: Confirm IRN and QR code fields where required and resolve rejected or mismatched imports.
- Return agreement: Compare final GSTR-1 outward-supply totals with the liability reported in GSTR-3B.
- Payment: Check the cash and input-tax-credit ledgers before offsetting liability and save the filing acknowledgement.
- Nil periods: File the required nil returns instead of assuming the portal will close the period automatically.
Which records should I keep for a reliable GST process?
Maintain a single period folder, electronic or paper-backed, containing invoices, credit and debit notes, order exports, operator statements, e-invoice downloads, reconciliation workpapers, payment references, and filed-return acknowledgements. Use stable file names that include the GSTIN, financial year, tax period, and report type.
Electronic records make searching and matching faster; a paper or offline backup helps when the billing system or internet connection is unavailable. Whichever medium you use, protect the invoice-number register and ensure that a backup cannot silently overwrite the original transaction history.
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How should I correct a mismatch after filing?
Do not alter a previously filed return’s evidence or delete the original invoice record. Identify whether the difference came from an order import, tax calculation, customer detail, credit note, TCS statement, or timing issue; document the cause and use the amendment or adjustment facility available in the relevant subsequent period and portal workflow.
For an e-invoice error, follow the IRP’s permitted cancellation or correction path before trying to change the return data. For a marketplace mismatch, obtain the operator’s detailed report and retain the correspondence or ticket number with your reconciliation file.
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Do I have to file a GST return if my marketplace account was inactive?
Yes, an inactive account does not by itself close the GST tax period. Check for any fees, returns, advances, credit notes, or other reportable entries, then submit the applicable nil or liability returns for the period.
Can my marketplace’s invoice be used as my GST invoice?
Only if it is issued by the correct supplier and contains the prescribed GST particulars, including the controlled serial number, supplier details, recipient details where applicable, HSN or service code, values, tax, and place-of-supply information. A settlement statement or packing slip alone is not a substitute.
What is the practical difference between an IRN and an invoice number?
The invoice number is your own consecutive series for the GSTIN and financial year. An IRN is the registration reference generated by the Invoice Registration Portal for an e-invoice; where e-invoicing applies, both references belong on the transaction record.
Why does my marketplace payout not equal the taxable sales in GSTR-1?
The payout can be reduced by commissions, shipping charges, refunds, cancellations, and TCS before money reaches your bank account. Reconcile the gross order and tax values to invoices first, then separately account for deductions and TCS rather than treating the net payout as sales.
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