Accounting integrations for multi-channel e-commerce sellers

Selling on multiple channels is great for revenue. It's less great for your bookkeeping.

Orders come in from Amazon, bol.com, your webshop, maybe a B2B portal. Each needs an invoice. VAT needs tracking correctly. Your accountant needs clean, reconcilable data. And somewhere in between, you're supposed to actually run your business.

The connection between your sales channels and your accounting software is where hours disappear. Get it wrong, and you're manually exporting, copying, and entering data every week. Get it right, and invoices flow automatically while you focus on selling.

What multi-channel sellers actually need

Forget feature lists. For e-commerce accounting integration, three things matter:

Automatic invoicing. When an order ships, an invoice should generate and land in your accounting software. No manual steps, no copy-pasting customer details, no forgetting to send one.

Correct VAT handling. Selling across EU borders means different VAT rates, thresholds, and reporting requirements. Your integration needs to handle this—or you'll spend hours fixing it later.

Clean data for your accountant. At the end of the month (or quarter), your accountant needs to reconcile everything. If your accounting software is full of messy, duplicated, or incomplete entries, that's your problem to solve—usually at the worst possible time.

The Dutch and Belgian landscape

If you're selling from the Netherlands or Belgium, you're probably not using QuickBooks or FreshBooks. The local market has its own tools: Exact Online, Moneybird, e-Boekhouden, Snelstart, Yuki, Twinfield, and plenty more.

The challenge is that most inventory and order management tools focus on US/UK accounting software. Dutch and Belgian sellers end up with workarounds, manual exports, or no integration at all.

How Stockpilot handles accounting

Stockpilot integrates with Webwinkelfacturen, which connects to over 20 Dutch and Belgian accounting packages. When an order is fulfilled in Stockpilot, the invoice data flows through to your accounting software automatically. One integration, broad coverage.

This handles the invoicing side cleanly. Orders become invoices, VAT is calculated, and your bookkeeping stays current without manual work.

When you need more than invoices

Sometimes invoicing isn't enough. If you're using something like Exact Online Handel, you might want stock mutations to sync to your accounting system too—so your accountant sees the full picture of inventory value and cost of goods sold.

For these cases, Stockpilot connects via Zapier. You can build custom flows that push inventory data, purchase orders, or other events to wherever they need to go. It's not as plug-and-play as the Webwinkelfacturen integration, but it gives you flexibility when your setup requires it.

The practical takeaway

You don't need to become an accounting integration expert. But you do need to ask the right questions before committing to a setup:

Does it handle invoices automatically when orders ship? Does it calculate VAT correctly for where you're selling? Does it connect to the accounting software you actually use—not just the big international names? And if you need deeper sync, is there a path to make that happen?

Get those answers, and you'll save yourself from becoming an unpaid bookkeeper on top of everything else you do.