Shopify and LHDN e-Invoice in Malaysia: which sales are yours to submit

A Malaysian seller who runs a Shopify store and a Shopee shop is running two different arrangements, and LHDN treats them differently for e-Invoice. On your own store you sell to the customer directly. On a marketplace you sell through a platform that collects the money and issues the tax document. Sellers who miss that distinction usually miss it in one direction — they submit everything they sold, marketplace orders included, and those transactions end up e-invoiced twice. This guide explains who issues what, why, and how to keep the two streams apart without a spreadsheet.

Merchant of record is the question that decides it

Before any e-Invoice question, ask a simpler one: in this sale, who is the seller as far as the customer and the money are concerned? That is the merchant of record.

On your own Shopify store, it is you. Your business name is on the checkout, your terms apply, the payment gateway settles to your bank account, and the customer's complaint comes to you. On a marketplace, the platform stands between you and the buyer — it runs the checkout, holds the money, and pays you out later, net of its fees.

That difference is not a technicality about software. It is why the tax document for a marketplace order is not yours to raise, and why the one for your Shopify order is.

What LHDN publishes about e-commerce platforms

LHDN's e-Invoice guidance for e-commerce (as at July 2026) puts the e-Invoice obligation for transactions concluded through an online marketplace on the platform provider rather than on the individual seller. In practice the platform issues the e-Invoice to the buyer and a self-billed e-Invoice to the seller for what it owes them. The seller does not submit those same transactions again.

Sales through a channel you own — your Shopify store, your own website, your own storefront — are outside that arrangement. There is no platform provider standing in for you, so the ordinary rules apply and the e-Invoice is yours to issue, subject to your turnover phase and the current implementation timeline.

These are LHDN's rules, not ours, and the e-commerce guidance has been revised as the rollout has matured. Read the current e-Invoice Specific Guideline on LHDN's official pages before you build a process on it, and if your arrangement is unusual — dropshipping, an agency model, a platform that behaves differently from the norm — put the question to LHDN or your tax agent rather than reasoning by analogy from this guide.

The practical split, channel by channel

For most Malaysian sellers the line falls in the same place every time. Your Shopify store, your own website, a WooCommerce shop, a storefront your accounting system hosts — you are merchant of record, so those sales belong in your own e-Invoice submissions. Shopee, TikTok Shop and Lazada are marketplaces, so those orders are the platform's to e-invoice.

The awkward part is that both streams land in the same books. Your Shopify order and your Shopee order both become revenue, both affect stock, both show up in your profit and loss. Only one of them belongs in your MyInvois upload. If your e-Invoice process starts from "everything I sold this month", you will submit the marketplace orders too.

A related trap is the invoice number. Many sellers assume they can spot marketplace sales by their reference — anything starting SHOPEE- or TIKTOK-. That works until a marketplace sale gets recorded with an ordinary invoice number, which happens more often than you would expect: a manual entry, a refund adjustment, an order keyed in by hand while an integration was down. The safer test is the channel recorded against the sale, not the shape of its reference.

Individual or consolidated: what to do with your own-store sales

Once you know which sales are yours, the next question is how they go in. A business customer who needs the e-Invoice for their own records will ask for an individual validated e-Invoice, and you issue one. A consumer buying a RM89 item from your Shopify store usually will not ask at all.

LHDN's rules allow qualifying sales to be aggregated into a periodic consolidated e-Invoice rather than raised one by one, with exceptions. Certain transaction types are carved out, and a single transaction above a stated value still needs its own e-Invoice even where the buyer never asked. The detail has moved during the rollout, so check the current guideline rather than a figure you remember.

Practically, that means an own-store seller wants a process that can do both: raise an individual e-Invoice when a buyer requests one, and roll the rest into a periodic consolidated submission. Building only the first leaves you raising hundreds of documents nobody wanted. Building only the second leaves you stuck the first time a company asks for a proper e-Invoice.

What your Shopify data is missing, and when you find out

A Shopify order carries a name, an email, a shipping address and a payment. An e-Invoice for a business buyer wants more than that: their tax identification number, a business registration number or NRIC, and a complete address including the state in LHDN's own code list. A phone number that is too short can be enough to stop the portal accepting the document.

This is where a lot of first submissions fail, and the failure is expensive because the portal rejects the rows rather than telling you in advance. The fix is unglamorous: collect the buyer details before you submit, not after the upload bounces. Software that checks the batch before you export — and names the buyer and the exact field that is missing — saves you the round trip.

The same applies to your own supplier details. Your business's tax identification number, registration number, industry code, address, state and contact number all sit on the document as the supplier block, and a single missing field there can invalidate every row in the file rather than one.

How Taokeh handles it

Taokeh, the Malaysian SME accounting software by Enya Venture, applies the split described above automatically. Sales from your own channels — Shopify, the Taokeh storefront, WooCommerce — appear on your MyInvois export with the rest of your invoices. Sales imported from Shopee, TikTok Shop or Lazada are kept off it, and off your consolidated document, so you cannot submit what the platform has already submitted.

Two checks enforce that, not one: the order reference and the channel stamped on the sale itself. The second check exists because a marketplace sale carrying an ordinary invoice number once reached an export when only the reference was tested. Both markers now have to be clear before a sale goes near the file.

What Taokeh does not do is submit for you. It builds the batch file in the format the MyInvois portal expects, blocks the export while a mandatory supplier or buyer field is missing and names what is missing, and gives you a monthly consolidated lane that generates one document per month and channel. You upload the file to MyInvois yourself and paste the validation link back into Taokeh, which reads the UUID and long ID out of it and stamps the MyInvois validation QR onto the invoice PDF your customer receives. Submitting to LHDN is your step; everything either side of it is handled. We would rather say that plainly than imply an automation that does not exist.

Underneath, it is one ledger. The Shopify order, the journal entry it posts, the gateway payout that settles it net of fees, and the e-invoice export are the same records in the same system, so month end is a matter of reading your books rather than reconciling a connector against them.

Frequently asked questions

Updated July 2026

This guide is general information for Malaysian SMEs, not tax, legal or accounting advice. Always confirm current rules and figures with the relevant authority or your own adviser.

Related guides

• LHDN e-Invoice (MyInvois) for Malaysian SMEs: a plain-English guide
• Payment gateway fees & reconciliation for Malaysian businesses
• SST in Malaysia for SMEs: registration, sales tax vs service tax, and SST-02

Related sources

• LHDN / HASiL — e-Invoice (MyInvois)
• LHDN / HASiL (Inland Revenue Board of Malaysia)