Compliance
How Shopify e-Invoicing Works in Malaysia (LHDN MyInvois)
By WebCEO Editorial · Published 16 October 2026
The short answer
A Shopify store in Malaysia issues e-invoices by connecting its orders to LHDN's MyInvois system through an app. Each online or POS order becomes an e-invoice that LHDN validates and stamps with a QR link. B2C sales where the buyer does not ask for an individual e-invoice can be grouped into one consolidated e-invoice, submitted within 7 days after month end.
Shopify does not talk to LHDN on its own. If your Malaysian company sells on Shopify, online or through Shopify POS, something has to turn each order into an e-invoice, send it to MyInvois, and keep the validation record. This guide explains how that works end to end, what has to be set up, and where the common mistakes are.
Key facts
- LHDN (Inland Revenue Board of Malaysia) runs the MyInvois system that validates every e-invoice.
- e-Invoicing has been phased in by annual turnover band since August 2024. Check the LHDN e-Invoice guideline for the current phase and threshold for your company.
- A validated e-invoice carries an LHDN validation link and QR code.
- B2C sales where the buyer does not request an individual e-invoice can be grouped into a consolidated e-invoice, submitted within 7 days after month end.
- Shopify has no built-in MyInvois submission. A connector app does the work.
- The WebCEO E-Invoice Malaysia app covers online and POS orders. It costs USD 24 per month on the Shopify App Store with a 7-day free trial.
What is e-invoicing in Malaysia?
e-Invoicing in Malaysia is the process of sending each sales invoice to LHDN’s MyInvois system, where it is validated and given a unique identifier before it counts as a valid invoice. It replaces paper or PDF invoices as the record of a sale for tax purposes.
The validated e-invoice includes a validation link and a QR code. A buyer can scan the code and confirm with LHDN that the invoice is genuine. The seller keeps the validated record as part of its tax documentation.
The rollout is by annual turnover band. Larger companies started first in August 2024 and smaller bands followed. Do not rely on a date you read in a forum post. Check the LHDN e-Invoice guideline for the phase and threshold that applies to you.
Does every Shopify order need its own e-invoice?
No. Only orders where the buyer requests an e-invoice, or where the buyer is a business, need an individual e-invoice. The rest of your B2C sales can go into one consolidated e-invoice for the month.
In practice a Shopify store has three kinds of orders:
- Individual e-invoice required. The buyer provided a TIN and business details, or asked for an e-invoice after purchase. Submit an individual e-invoice.
- Consolidated. Walk-in or online shoppers who did not ask. These are grouped and submitted as one consolidated e-invoice within 7 days after month end.
- Adjustments. Refunds, exchanges and price corrections, handled with credit, debit or refund notes against the original e-invoice.
The hard part is not the submission. It is knowing which bucket each order belongs in, and letting a customer move an order from the consolidated bucket to the individual one without your staff doing data entry.
How does an e-invoice get from Shopify to LHDN?
An app reads the Shopify order, maps it to the LHDN e-invoice fields, submits it to MyInvois, and writes the validation result back to the order. The WebCEO E-Invoice Malaysia app does this in three steps: Install, Configure, Automate.
- Install. Add the app from the Shopify App Store to your store.
- Configure. Enter your company details and TIN, map Shopify tax settings and product classifications to the LHDN schema, and decide the default treatment for online and POS orders.
- Automate. New orders flow to MyInvois without manual work. Individual e-invoices are submitted when the order qualifies. Everything else is held for the consolidated submission.
For each order the app records the submission status, the LHDN validation link and QR, and any error returned. If LHDN rejects a submission because a field is missing or malformed, the order shows as unsubmitted so you can fix it before the deadline.
Customer requests. Customers request an e-invoice through a self-service portal, in one click, from their phone. They do not need to email your team.
This matters for retail. A customer who bought at the counter and later needs an invoice for their company claim can scan a QR at the store or follow a link from their receipt, enter their details, and trigger the individual e-invoice. The app then removes that order from the consolidated batch and submits it on its own. Staff are not involved.
For online orders the same portal works from the order confirmation. The buyer fills in TIN and business details once, and the e-invoice is generated against that order.
POS sales in physical outlets. Shopify POS orders are treated the same way as online orders. The app reads them from Shopify, so a sale made on an iPad at your outlet in a mall is captured without separate software at the counter.
This is the main reason to keep POS and online on one platform. One order record, one customer record, one e-invoice pipeline. If your outlets run a separate POS system, you need a second integration and a second reconciliation.
Most retail counter sales end up in the consolidated e-invoice. The exceptions are business buyers and customers who request an invoice through the portal. If you run Shopify POS in a shopping mall, the same order data also feeds your mall GTO sales submission. See /shopping-mall-gto for how that works.
How do refunds, exchanges and cancellations work?
A refund, exchange or price correction against a validated e-invoice is handled with a credit note, debit note or refund note that references the original e-invoice. You do not edit or delete the original.
- Credit note. Reduces the value of the original e-invoice, for example a partial refund or a returned item.
- Debit note. Increases the value, for example an additional charge added after the sale.
- Refund note. Records money returned to the buyer.
The app generates these from Shopify’s refund and order-edit events, so the note matches what actually happened in your store records.
What does the monthly cycle look like?
Each month the merchant reviews a consolidated report of submitted and unsubmitted e-invoices, fixes any failures, and submits the consolidated e-invoice for B2C sales within 7 days after month end.
A typical month:
| When | What happens |
|---|---|
| Daily | Individual e-invoices submitted automatically for qualifying orders. Customer requests processed through the portal. |
| Daily | Credit, debit and refund notes generated from refunds and order edits. |
| Month end | Consolidated report lists every order, its status, and anything unsubmitted. |
| Within 7 days after month end | Consolidated e-invoice submitted for B2C orders that were not individually invoiced. |
| Ongoing | Submission reports and audit records kept for every e-invoice and note. |
The audit record is the part people skip and then regret. When LHDN asks about a transaction, you need the submission time, the response, the validation identifier and the matching Shopify order in one place.
How much does Shopify e-invoicing cost?
The WebCEO E-Invoice Malaysia app has three plans plus a one-time setup fee. Choose by daily volume and reporting needs.
| Plan | Price | Included |
|---|---|---|
| Standard | USD 24 per month, or USD 240 per year | Up to 100 e-invoice submissions per day, self-service portal, consolidation, credit and refund notes, automatic LHDN validation, works with POS |
| Trial | Free for 7 days | Full Standard features |
| Enterprise | Custom | Multi-location, dedicated account manager |
| High volume | Quoted | More than 100 submissions a day or multiple locations |
All plans include online and POS order coverage, the customer self-service portal, the monthly consolidated report and submission, credit, debit and refund notes, submission reports and audit records.
What should you set up before going live?
Before switching on e-invoicing, confirm your company data in Shopify is complete and consistent, because every missing field becomes a rejected submission.
- Company name, registration number and TIN match your LHDN registration.
- Shopify tax settings reflect the taxes you actually charge.
- Products carry the classification the LHDN schema expects.
- Customer records for B2B buyers include TIN and registration details.
- Refund and exchange workflows in Shopify POS are used consistently so notes are generated correctly.
- Staff know how to point a customer to the self-service portal instead of taking details by hand.
Run a short test period with a handful of orders and check the validation results before you rely on automation for the whole store. If your store needs custom fields or a different checkout flow to capture buyer details, that is development work. See /shopify-development.
Common mistakes. Most problems we see come from data, not from the submission itself.
- Treating every POS sale as an individual e-invoice and overloading the team with data entry.
- Missing the 7-day window for the consolidated submission because nobody reviewed the unsubmitted list.
- Editing an order after the e-invoice was validated instead of issuing a credit or debit note.
- Running separate POS and online systems, then trying to reconcile two sets of invoices.
- Taking a customer’s TIN by hand at the counter and typing it in later, with errors.
Where WebCEO fits
WebCEO builds and runs Shopify stores for Malaysian retailers, and the WebCEO E-Invoice Malaysia app on the Shopify App Store is how those stores submit to LHDN MyInvois from both online and POS orders. We set it up, map your tax and product data, and support the monthly cycle. If you are still deciding whether your store should be on Shopify at all, see /shopify-pricing and /shopify-support, or go straight to /e-invoice to see the app in detail and /contact to talk to us.
Sources
Does Shopify submit e-invoices to LHDN by itself?
No. Shopify has no built-in MyInvois submission step. A connector app such as WebCEO E-Invoice Malaysia reads each Shopify order, formats it to the LHDN schema, submits it and stores the validation result against the order.
Do I need an e-invoice for every walk-in sale on Shopify POS?
No. B2C sales where the buyer does not request an individual e-invoice can be grouped into a consolidated e-invoice submitted within 7 days after month end. Buyers who want one can request it themselves through a self-service portal.
What happens to refunds and exchanges?
A refund or price change against a validated e-invoice is handled with a credit note, debit note or refund note that references the original e-invoice. The app generates these from the Shopify refund or order edit.
Which businesses must issue e-invoices right now?
LHDN is phasing e-invoicing in by annual turnover band, starting in August 2024. Check the LHDN e-Invoice guideline for the current phase and threshold that applies to your company.
How much does the WebCEO E-Invoice Malaysia app cost?
USD 24 per month on the Shopify App Store, or USD 240 a year, with a 7-day free trial. The Standard plan covers up to 100 e-invoice submissions a day. Higher volumes are quoted by WebCEO.