E-Invoicing for E-Commerce Sellers in Malaysia — Shopee, Lazada, and Beyond

E-commerce sellers are not exempt

If you sell products online in Malaysia — whether through Shopee, Lazada, TikTok Shop, your own Shopify store, or Instagram DMs — LHDN's e-invoicing mandate applies to you. There is no exemption for online businesses, small sellers, or marketplace-based operations.

This creates real challenges for e-commerce sellers that traditional businesses do not face. You might process dozens or hundreds of orders per day, sell to anonymous consumers who never share a TIN, deal with returns and refunds at high rates, and receive payments through marketplace platforms that deduct commissions before paying you. Each of these situations has e-invoicing implications.

Understanding your e-invoicing obligations

As an e-commerce seller, you issue e-invoices in two directions:

1. You to your customers (sales)

Every sale you make requires an e-invoice. For B2C sales (individual consumers), you have two options:

• Individual e-invoices — One per transaction, using the general public TIN if the buyer does not provide theirs
• Consolidated e-invoices — Batch all B2C transactions for a period into a single e-invoice

For B2B sales (businesses buying from you), you must issue individual e-invoices with the buyer's TIN and BRN.

2. Marketplace to you (commissions and fees)

When Shopee, Lazada, or another marketplace deducts commissions, shipping fees, or marketing charges from your payouts, those deductions are expenses to you. The marketplace should be issuing e-invoices or tax invoices to you for their services.

B2C consolidation: the lifeline for high-volume sellers

Most e-commerce sellers do not know their buyers' TINs. A customer on Shopee provides a shipping address, not a tax identification number. For these B2C transactions, consolidated e-invoicing is your primary compliance mechanism.

How consolidated e-invoices work for e-commerce

Instead of submitting one e-invoice per order (which could mean 200+ submissions per day for an active seller), you batch all B2C sales into a single consolidated e-invoice.

Recommended approach: daily consolidation

Example consolidated e-invoice for a fashion seller:

You can summarize line items by product category rather than listing every individual SKU sold that day. The total must match your actual daily sales.

When a customer requests an individual e-invoice

LHDN requires that if a buyer requests an individual e-invoice and provides their TIN, you must issue one. This is more common for B2B purchases (a company buying supplies through Shopee, for example).

When this happens:

1. Issue an individual e-invoice for that specific transaction with the buyer's TIN and BRN
2. Exclude that transaction from your daily consolidated e-invoice
3. Submit both the individual e-invoice and the consolidated e-invoice (minus that transaction) to MyInvois

Marketplace-specific considerations

Shopee sellers

Shopee processes payments and deducts commissions before paying sellers. Your e-invoicing workflow needs to account for:

• Gross sales — The total amount customers paid (this is your revenue for e-invoicing purposes)
• Shopee commission — Typically 2-5% depending on your seller tier and category
• Payment processing fees — Additional percentage deducted per transaction
• Shipping subsidies — Shopee sometimes subsidizes shipping; this affects the shipping amount on your invoice
• Voucher absorptions — If you funded a seller voucher, the discounted amount is your actual revenue

Your e-invoice should reflect the amount the customer paid, not the net amount Shopee sends you. The commissions and fees are separate expenses (which Shopee should invoice you for).

Example:

• Customer pays RM 100 for a product
• Shopee deducts RM 5 commission + RM 2.12 payment fee
• You receive RM 92.88

Your sales e-invoice is for RM 100 (the customer's purchase price). The RM 7.12 in fees is a separate expense transaction between you and Shopee.

Lazada sellers

Lazada operates similarly to Shopee, with commission deductions, marketing fees, and logistics charges. The same principle applies: invoice the gross sale amount, and account for platform fees separately.

Lazada's seller center provides transaction reports that break down each order into gross amount, commission, fees, and net payment. Use these reports to reconcile your e-invoices.

TikTok Shop sellers

TikTok Shop is newer but growing rapidly in Malaysia. The commission structure and payout process follow similar patterns to Shopee and Lazada. Key difference: TikTok Shop often involves affiliate commissions (paid to content creators who promote your products), which are an additional deduction from your payout.

Your own website (Shopify, WooCommerce, etc.)

If you sell through your own website, you have more control over the e-invoicing process because you handle payments directly. The workflow is simpler:

1. Customer places an order and pays
2. Your system generates an e-invoice (B2C consolidated or individual if TIN provided)
3. E-invoice is submitted to MyInvois
4. Customer receives an order confirmation with the e-invoice reference

The advantage of selling on your own platform is that you can integrate e-invoicing directly into your checkout flow.

Handling returns and refunds

E-commerce has higher return rates than traditional retail. In Malaysia, Shopee's 15-day return policy and similar marketplace guarantees mean that a meaningful percentage of your sales will be reversed. E-invoicing must account for this.

Return within 72 hours of e-invoice validation

If the return and refund happen within 72 hours of the e-invoice being validated by LHDN:

• For individual e-invoices: Cancel the e-invoice through MyInvois
• For consolidated e-invoices: You typically cannot cancel the consolidated invoice. Instead, issue a credit note for the returned item

Return after 72 hours

If the return happens after the 72-hour window (which is common — most marketplace returns take several days to process):

• Issue a credit note referencing the original e-invoice
• The credit note covers the refunded amount including any tax

Partial refunds

Marketplace disputes sometimes result in partial refunds (e.g., the customer keeps the product but receives a RM 20 goodwill credit). Issue a credit note for the partial refund amount.

Tracking returns for consolidated invoices

This is the tricky part. If you submitted a consolidated e-invoice for Tuesday's sales, and a customer from Tuesday requests a return on Friday, you need to issue a credit note that references Tuesday's consolidated e-invoice. Keep records of which orders were included in which consolidated e-invoice.

When ORD-4523 is returned on Feb 7, you issue a credit note referencing CONS-2026-0203.

Cross-border e-commerce

If you sell to customers outside Malaysia (via Shopee International, Lazada CrossBorder, or your own international shipping), additional considerations apply:

Exported goods

Goods physically shipped out of Malaysia may qualify for zero-rated SST treatment. You still submit an e-invoice to MyInvois, but the tax amount is RM 0.00. Ensure you have documentation (shipping manifests, customs declarations) to support the zero-rating.

Goods from foreign sellers

If you are a Malaysian buyer purchasing from a foreign Shopee or Lazada seller, the foreign seller may not submit e-invoices to MyInvois. For significant business purchases from foreign suppliers, you may need to issue a self-billed invoice.

Multi-currency orders

If you list products in USD or SGD on international marketplaces, you need to handle currency exchange rates in your e-invoices. The e-invoice must include the exchange rate to MYR and calculate tax in Ringgit.

Vouchers, discounts, and promotions

E-commerce platforms run constant promotions — platform vouchers, seller vouchers, flash sales, bundle deals, free shipping campaigns. Each affects your e-invoice amounts differently.

Platform-funded vouchers

If Shopee or Lazada funds the voucher (e.g., a RM 10 platform voucher), you receive the full product price from the marketplace. Your e-invoice reflects the full price the customer paid before the voucher. The voucher is a matter between the customer and the platform.

Seller-funded vouchers

If you fund the voucher (e.g., you offer a RM 5 seller discount), the customer pays less, and you receive less. Your e-invoice should reflect the actual amount paid by the customer after your discount.

Example:

• Product price: RM 50.00
• Seller voucher: -RM 5.00
• Customer pays: RM 45.00
• Your e-invoice amount: RM 45.00

Bundle deals

For "buy 2 get 1 free" or bundle pricing, the e-invoice should show the actual amount charged for the bundle, with line items reflecting the individual products and their allocated prices.

Free shipping absorbed by seller

If you absorb shipping costs (the customer sees "Free Shipping" but you pay the courier), shipping does not appear on the customer's e-invoice since they were not charged for it. However, the courier's invoice to you is a separate expense.

Practical workflow for e-commerce e-invoicing

Here is a realistic daily workflow for an active e-commerce seller:

End of each business day

1. Export your order data — Download the day's completed orders from your marketplace seller center or e-commerce platform
2. Separate B2B from B2C — Any orders where the buyer provided a TIN get individual e-invoices. Everything else goes into the consolidated batch
3. Create consolidated e-invoice — One document covering all B2C sales for the day, summarized by product category
4. Submit to MyInvois — Send all e-invoices (individual + consolidated) to LHDN
5. Process returns — For any returns from previous days, issue credit notes referencing the appropriate original e-invoice

Monthly reconciliation

At the end of each month:

• Compare your total e-invoice amounts against marketplace payout reports
• Verify that commissions and fees received from platforms match your expense records
• Ensure all returns have corresponding credit notes
• Check for any rejected submissions that need resubmission

Common mistakes e-commerce sellers make

1. Invoicing the net payout instead of gross sales — Your e-invoice should reflect what the customer paid, not what the marketplace paid you after deductions.

2. Forgetting to exclude individual e-invoice orders from consolidation — If you issued a separate e-invoice for a B2B order, do not also include it in the consolidated e-invoice. This creates double-reporting.

3. Not issuing credit notes for returns — Every refund needs a corresponding credit note in MyInvois. Returns that are not documented create discrepancies between your reported revenue and your actual income.

4. Using marketplace order IDs as invoice numbers — Marketplace order IDs may not be unique across platforms or may conflict with your numbering system. Use your own sequential invoice numbering.

5. Ignoring platform fees as expenses — Marketplace commissions are tax-deductible expenses. Ensure the marketplace is issuing proper tax invoices for their services.