Shopify integration with SQL Account and AutoCount

Retailers that run SQL Account or AutoCount behind a Shopify store usually start from the same place: someone re-keys Shopify orders into the accounting system at the end of each day, and stock counts drift apart between the two. This guide covers what an integration should sync, in which direction, and the decisions to make before anyone writes code.

What should sync between Shopify and the accounting system?

Products, stock, orders, payments and customers. Each needs one owner and one direction.

The most common arrangement looks like this:

Record	Usual source of truth	Direction	Notes
Products and item codes	Accounting system	Accounting to Shopify	Shopify holds the descriptions and images; the item code links the two
Prices	Either	One way only	Pick one system for price changes, or they will overwrite each other
Stock levels	Accounting system or Shopify	One way, per location	Decide per warehouse and outlet
Online orders	Shopify	Shopify to accounting	Posted as sales orders, cash sales or invoices
POS sales	Shopify	Shopify to accounting	Per outlet, often summarised daily
Payments and refunds	Shopify and the payment provider	Shopify to accounting	Refunds post as credit notes
Customers	Shopify for online buyers	Shopify to accounting	Often only business buyers or debtor accounts

Two-way sync of the same field sounds attractive and causes most of the problems. If staff can change a price in both systems, the integration has to guess which change wins. A written field-by-field contract avoids that.

How should POS sales be handled?

As Shopify orders tied to an outlet, posted to the accounting system per location.

With Shopify POS, an in-store sale is an order in the same Shopify account, linked to the outlet's location. That means one integration can carry online and in-store sales. The choice is how much detail to post. Posting every receipt keeps line-level history in the accounting system. Posting one daily summary per outlet keeps the ledger lighter but leaves the detail in Shopify. Whichever you pick, stock deductions must still happen per item, or the accounting system's stock will drift.

Who should issue the LHDN e-invoice?

Either the accounting system or a Shopify app, never both for the same sale.

Malaysian e-invoices are submitted to LHDN's MyInvois system. Both accounting vendors and Shopify apps can do this, which creates a real risk of submitting the same sale twice. The two approaches:

	Accounting system issues	Shopify app issues
How it works	Orders post to SQL Account or AutoCount, which submits to MyInvois	A Shopify app submits from the order, before or alongside posting to accounts
Customer requests	Handled after the order reaches accounts	Customer can request from the order page or receipt
Consolidated monthly e-invoice	Generated in the accounting system	Generated by the app from Shopify sales
Strength	One place for all e-invoices, including non-Shopify sales	Faster for buyers, and covers POS and online without waiting for the sync
Weakness	Customers wait for the order to sync before a request can be processed	Accounting system must record the e-invoice reference instead of resubmitting

Both vendors offer e-invoicing. SQL Account's documentation describes MyInvois submission, including consolidated e-invoices, and lets you set a customer's default submission mode to consolidated. AutoCount describes its e-Invoice Platform as covering standard, consolidated and self-billed e-invoices generated from AutoCount Accounting or Cloud Accounting. On the Shopify side, our e-invoice app handles customer requests from the order page or receipt QR code, POS and online sales, and monthly consolidation.

The rule of thumb: if most of your invoicing happens outside Shopify, let the accounting system own it. If Shopify carries most retail sales and customers ask for e-invoices at the counter, a Shopify app is usually simpler, and the integration passes the validated e-invoice reference to the accounting system.

This is software design, not tax advice. Confirm your obligations with LHDN's current guidelines and your tax adviser.

What do SQL Account and AutoCount expose for integration?

Both have documented REST APIs, with different setups.

SQL Account. E Stream MSC publishes the SQL Account API, a REST service that can create, edit, delete and retrieve records. Listed objects include sales invoices, sales orders, purchase invoices, customer payments, journal entries, customers, agents, stock items, stock received and stock transfers. Requests are signed with AWS Signature Version 4 using an access key and secret key generated for a dedicated API user. That user can no longer log in to SQL Account directly once a key exists. As listed on 18 October 2026, the API requires SQL Accounting 5.2025.1038.875 or above. It supports desktop, public cloud and private cloud setups, and on-premise or private cloud installations need a server and internet connection available around the clock.

AutoCount. AutoCount's Resource Center documents the AOTG API, a RESTful API for creating, updating, deleting and reading AutoCount Accounting data. Requests pass through an AOTG cloud server to an AOTG Client service installed on the computer that hosts the AutoCount Accounting server. Access needs an API key from activating the account book with AOTG, plus a user login, to obtain an access token. AutoCount also has a plug-in SDK for .NET development, which requires a Developer ID.

Shopify's side is the Admin API, with webhooks that notify an integration when orders, refunds or inventory change.

Which integration approach fits?

Off-the-shelf connector if one fits, middleware for moderate needs, custom code for anything specific.

1. Off-the-shelf connector. On 18 October 2026 we could not verify a Shopify connector listed by either vendor. Third-party connectors may exist. If you find one, check which records it syncs, whether it handles POS locations, and who supports it.
2. Middleware. An integration platform maps Shopify webhooks to accounting API calls. This works when the mapping is standard, but the accounting APIs' signing and local-client setups still need technical work.
3. Custom integration. A small service between Shopify and the accounting API, with logging, retries and alerts. It costs more to start and fits stores with several outlets, unusual item codes or e-invoice rules.

Whatever the approach, build for failure. The accounting server will be offline sometimes, especially when it sits on an office PC. The integration should queue changes and retry, not drop them.

Checklist before you start

• Which system owns products, prices, stock and customers?
• Do Shopify SKUs match accounting item codes exactly?
• How should online orders post: sales order, cash sale or invoice?
• Every receipt or a daily summary for POS outlets?
• Which system issues e-invoices, and how is the reference recorded in the other?
• How are refunds, exchanges and partial refunds posted?
• Where does the accounting system run, and is it reachable around the clock?
• Which version of SQL Account or AutoCount do you run, and does it meet the API requirements?
• Who gets alerted when a sync fails?

Frequently asked questions

Does SQL Account or AutoCount connect to Shopify out of the box?

We could not verify a vendor-listed Shopify connector for either on 18 October 2026. Both offer APIs, so an integration can be built against them.

Can stock sync in real time?

Close to it. Shopify sends webhooks when orders arrive, and the integration can update the accounting system within moments. Updates from the accounting system to Shopify depend on how often the integration polls or how changes are pushed.

Can both systems submit e-invoices?

They can, which is the risk. Choose one issuer per sale and pass the e-invoice reference to the other system.

What does WebCEO build here?

We build custom Shopify integrations for ERP and accounting systems, and run the WebCEO E-Invoice app for Shopify. To scope a SQL Account or AutoCount integration, talk to us.