Connecting Shopify to e-Boekhouden.nl
For almost every starter and sole trader with a Shopify shop, a standard app is the right route: there are three official partner apps, with subscriptions from $13.95 to $36 per month (Shopify App Store, 2026). The choice between the three comes down to details — refunds, history and Shopify Payments — because all three can post orders.
- Fixed monthly fee
- Fixed project price up front
- Microsoft and Google
- Response to your request within one business day
Which Shopify–e-Boekhouden connection suits you?
Three apps do essentially the same thing — turning your Shopify orders automatically into entries in e-Boekhouden.nl — and cost between $13.95 and $36 per month (Shopify App Store, 2026). On its own integrations page, e-Boekhouden.nl lists three partners: Online Origins, Webwinkelfacturen and Combidesk (e-Boekhouden.nl, 2026). That makes choosing confusing: three times roughly the same promise, three times a different price tag. The real difference is in the details — does the app also process refunds, can it handle order history, and do the Shopify Payments payouts flow into your books. Below we put the three apps side by side, plus the two alternatives: an automation tool and custom development. What such an automated flow looks like, you can see in the Flow Lab; what the custom route costs, you can read in What does an API integration cost?
If you work with SnelStart instead of e-Boekhouden.nl, read Connecting Shopify to SnelStart. If, alongside your webshop, you have a physical store with a Lightspeed till, then Connecting Lightspeed to Exact Online is the comparable story for the point-of-sale side. You'll find all combinations in the integrations overview.
Three apps and two alternatives side by side.
| Option | Type | Indicative cost | Suitable for |
|---|---|---|---|
| e-Boekhouden.nl Koppeling (Online Origins) | Standard app | $13.95 p/m, 14-day trial (Shopify App Store, 2026) | Starters and sole traders who want orders, VAT and discounts posted automatically |
| e-Boekhouden.nl (Webwinkelfacturen) | Standard app | $15.95 p/m, 30-day trial (Shopify App Store, 2026) | Anyone who also wants to import order history from before the connection |
| Combidesk e-Boekhouden.nl | Standard app | $18–36 p/m, 30-day trial (Shopify App Store, 2026) | Anyone who wants to post refunds and — in the more expensive variants — Shopify Payments payouts |
| Make / Zapier / Power Automate | iPaaS workflow | from $9 p/m in licences (Make, 2026) | Custom rules: a ledger per product group or multiple shops on one administration |
| Custom development on the API | Custom | indicative €1,500–€15,000 one-off (see What does an API integration cost?) | High volumes or posting logic no app supports |
App subscriptions via the Shopify App Store are billed in dollars. The amounts quoted are the monthly prices listed on the product pages in June 2026; check the current price and trial period before you choose — all three partners let you test for free first.
What does and doesn't sync with e-Boekhouden.nl?
Orders with VAT, discounts and shipping costs go across automatically with all three apps; products and inventory go across with none of them. The differences lie in refunds, payouts and history — precisely the points where the three apps diverge, and therefore the points on which you make your choice.
| Data | Standard app | Custom connection |
|---|---|---|
| Orders with VAT, discounts and shipping costs | Yes | Yes |
| Customer details with the order | Yes | Yes |
| Refunds and credit entries | Limited — Online Origins and Combidesk explicitly mention refund processing; test this during the trial period | Yes |
| Shopify Payments payouts and transaction fees | Limited — only in the more expensive Combidesk variants | Yes |
| Custom ledger lines per product group or country | Limited — you choose from the app's fixed settings | Yes |
| Products and inventory | No — these apps post revenue, not inventory | Optional |
| Order history from before the start date | Limited — the Webwinkelfacturen app can import history | Optional |
Three questions that decide the choice.
Does your administration fit within an app's settings?
Do you sell mainly within the Netherlands, with standard VAT rates and one shop on one administration? Yes → choose one of the three apps and use the trial period to test your edge cases. No → move on to question two.
Do you only want to post revenue, or also reconcile payouts?
Revenue only → the cheapest app is enough. Also processing the Shopify Payments payouts and transaction fees automatically → the more expensive Combidesk variant, or custom work if you want to go beyond a single payment provider.
Do you have custom rules or multiple sales channels?
No → a standard app. Yes — a ledger per product group, multiple shops or marketplaces on one administration — → an automation tool or a custom connection on the API.
The rule of thumb: choose the cheapest app that demonstrably covers your three most important scenarios, and only move to custom work once your rules or volumes fall outside the app settings.
Where this connection goes wrong in practice.
Choosing on price instead of on scenarios
The three apps differ by a few dollars a month — irrelevant against a single refund scenario that doesn't work. Test your real edge cases during the trial period: a return, a discount code, a foreign order.
Overlooking VAT outside the Netherlands
Sales to consumers in other EU countries fall under the OSS scheme, with VAT rates per country. Before going live, check that the app writes those scenarios away correctly, otherwise the connection makes your return wrong instead of easy.
Payouts stay manual work
Most apps post orders, not the payouts from your payment provider minus transaction fees. Reconciliation then stays manual work; take this explicitly into account in your choice or have it included in custom work.
No one checks whether the connection is still running
An app that fails silently isn't noticed until the VAT return. Agree who periodically checks that the entries come in and reconcile — or have the connection monitored as part of management.
What webshop owners ask us beforehand.
What does a Shopify–e-Boekhouden connection cost?
The three standard apps cost between $13.95 and $36 per month, depending on the supplier and plan (Shopify App Store, 2026). If you have the setup and testing done for you, that usually falls in the range of an indicative €500 to €2,000. Custom development on the API costs an indicative €1,500 to €15,000 one-off, depending on the logic and volumes.
How quickly is the connection live?
A standard app is technically running within an hour, but count on a few days to a week to properly configure and test ledger accounts, VAT rates and edge cases such as returns and discounts. A custom connection takes several weeks instead, mainly because of the testing work.
What if the app stops or can no longer handle my volume?
Your bookkeeping simply stays put: the entries already in e-Boekhouden.nl are not lost. You then switch to a different app or to custom development. Because all three apps run on the same e-Boekhouden API, switching is mainly a matter of reconfiguring and testing — not a migration of your records.
Who keeps an eye on whether the connection keeps running?
By default, no one — that is the honest summary. The apps usually report errors by email, but that email does have to be read. Agree internally who periodically checks that the entries reconcile, or have the connection managed and monitored externally, for example as part of a management arrangement.
Do I need to switch from e-Boekhouden.nl to another package?
No. e-Boekhouden.nl has a public API and three official Shopify partners, so for a standard webshop administration there is no reason to switch. Only once your needs grow structurally larger — inventory management, multiple entities, extensive reporting — does a package change become worth considering, but that is separate from this connection.
Help with the choice or the setup?
We'll look with you at which route fits your volume and administration, set up the connection and test the edge cases — or build custom work if the apps don't fit.