Top 5 Automated Invoicing Extensions for E-Shops

Malaysian e-shops now live inside the LHDN e-invoice schedule. Phase 1 companies (annual turnover above RM100 million) entered the live MyInvois portal in August 2024; Phase 2 turnover band (RM25 million to RM100 million) followed in January 2025; every remaining business joined before 1 July 2025. That means the invoicing app on your storefront is no longer just a PDF generator. It has to map checkout data to the validation fields LHDN checks: supplier TIN, SST registration number, buyer ID type, MSIC product classification, and the exact tax split. The five tools below do that mapping locally, not inside a generic cloud middleware.

1. Zoho Books for Shopify

The official Zoho Books app for Shopify listens to order webhooks and creates draft sales invoices before your courier labels are even printed. It then applies the registered SST tax code from your Zoho Books organisation and stamps each invoice with a sequence number that matches LHDN’s “Inv-YYYY-MM-XXXX” format. For e-shops that already run Zoho Books as their main ledger, this removes the rekeying step entirely. The app also reads the customer’s NRIC, business registration number, or passport number from the Shopify checkout field and puts it directly into the e-invoice buyer ID block.

Zoho’s Malaysia tax edition supports the MyInvois API, so submitted e-invoices return the LHDN validation ID and QR code automatically. This is the strongest pick if your finance team already lives in Zoho Inventory or Zoho CRM.

2. Bukku

Bukku is built for the local seller who does not want to reconcile a foreign accounting package. The e-commerce link within Bukku pulls orders from Shopify, WooCommerce, and EasyStore through their public APIs and stages them as sales invoices inside Bukku’s Sales module. You review the queue, click confirm, and Bukku submits them directly to MyInvois.

There is one strong regional advantage: Bukku handles the consolidated e-invoice flow. B2C transactions from a full month of shop orders are merged into a single LHDN-compliant consolidated invoice per buyer type, which is what LHDN’s implementation guidelines expect for lower-volume sellers. Its monthly plan sits under RM100, making it the most practical entry for a KL-based e-shop running under 300 orders per month.

3. AutoCount eCommerce + E-Invoice

AutoCount is already the default accounting engine for many Malaysian bookkeeping firms. The AutoCount eCommerce module is a connector that talks to Shopee, Lazada, and TikTok Shop APIs, then drops the order data straight into AutoCount’s Sales Invoice workflow. This is critical because those three marketplaces carry most of the transaction volume on Malaysian storefronts, and manual CSV importing fails when daily order counts exceed 200.

The E-Invoice module in AutoCount submits to MyInvois and also supports PEPPOL channels for orders that cross into Singapore. For a shop selling through multiple marketplaces, AutoCount gives you per-channel invoice series numbering so you always know whether an invoice came from Shopee or from your WooCommerce site.

4. Odoo Accounting with the Shopify Connector

Odoo is the pick when your e-shop also runs a warehouse. The official Shopify connector synchronises order data into Odoo’s Sales module, and once inventory picking is done, the confirm action generates the invoice automatically. Downstream, the Odoo localisation pack for Malaysia handles SST transactions and passes e-invoice payloads to MyInvois via the LHDN API endpoint.

Because Odoo is open source, the community has built additional bridges for Shopee and Lazada that run as add-on modules inside the same database. This avoids the dual-system pain of keeping invoices in one log and stock in another. The accounting feature set is free for one month, and the connector runs as a subscription; the real cost is getting the localisation modules configured by a KL partner.

5. SQL Account eBusiness Connect

SQL Account is the closest thing to a default local accounting engine for Malaysian shops that started with UBS-era habits. The eBusiness Connect plugin converts incoming online orders to Stock Issue transactions and then to Sales Invoices, in the same keypress sequence an operator would use for a counter sale. This is a workflow built for people who prefer grid-based reconciliation over app-store minimalism.

The native e-Invoice module in SQL Account reads the sales invoice data and submits it to MyInvois with the required document code and transaction code, including the consolidated variant for B2C sales. For B2B e-shops — the kind selling packaging, stationery, or ingredients to KL F&B operators — this is a safe fit because buyers expect a full e-invoice record in their own supplier file.