If you're running an online store from the Netherlands, bookkeeping for e-commerce businesses looks deceptively similar to any other small business at first: invoices in, invoices out. The difference shows up once you actually sell from stock, get paid through a payment processor instead of directly, and possibly sell through more than one channel at once. Get any of those three wrong and both your VAT return and your profit figure stop matching reality.
What makes bookkeeping for e-commerce businesses different?
Three things make e-commerce bookkeeping different from a service business that doesn't hold inventory:
- Inventory valuation: what you buy in isn't a cost yet until it's actually sold.
- Payment processors: Mollie, Stripe or PayPal pay out a batched amount, not per individual sale.
- Multiple sales channels: your own site, social commerce, and sometimes a marketplace, all at once.
Inventory and cost of goods: why your real profit isn't what your bank balance shows
Buy in 100 units and sell 40 of them this month, and only the cost of those 40 units belongs in this month's costs. The other 60 sit on your balance sheet as inventory, not in your profit and loss statement. Book the full purchase invoice as an expense the moment it arrives, and your profit looks artificially low in the buying month and artificially high in the months you actually sell. VAT isn't affected by this, you still reclaim it when the purchase invoice comes in, but an accurate profit and loss statement and annual accounts need a current inventory count, not just a pile of purchase invoices.
Payment processors: gross sales versus what actually lands in your account
A marketplace like Bol.com or Amazon deducts commission and fulfilment costs before paying out. A payment processor on your own webshop works differently again: Mollie, Stripe or PayPal typically pay out a batched amount daily or weekly, net of a small transaction fee per payment. Book only the number that hits your bank account and you'll miss the transaction fees as a separate cost, and you'll likely double-count or completely miss refunds along the way. Work from your payment processor's own dashboard export, not the bank statement alone.
One bookkeeping system for several sales channels
Sell through your own site plus Instagram Shopping, a pop-up, or a marketplace, and it's tempting to track each channel separately and only reconcile at the end. That works fine until a customer returns an order through a different channel than they bought it on, or until you need to work out how much VAT you've already remitted per channel at quarter-end. Set up one revenue ledger with a column or cost centre per channel instead, so you can always report per channel and in total without reconstructing anything after the fact.
A worked example: from processor payout to bookkeeping entry
| Item | Amount |
|---|---|
| Gross sales this week via Mollie | €2,600 |
| Transaction fees (roughly 1.5% + a fixed amount per payment) | - €58 |
| Refunded orders | - €120 |
| Net amount deposited to your account | €2,422 |
The €2,600 gross figure is your revenue for VAT purposes, not the €2,422 that actually reaches your account. Transaction fees get booked separately as a business cost; refunds reduce revenue in the period the refund happened, not the period of the original sale.
Frequently asked questions
Do I charge VAT on shipping costs I pass on to customers? Yes, shipping costs you charge a customer follow the VAT rate of the product being shipped. If your order mostly contains goods at the reduced rate, the shipping cost in that order follows the same reduced rate.
How do I book inventory that's still unsold at year end? Value it at purchase cost (or lower market value if it's aged or damaged) and list it as an asset on your balance sheet. The cost of that inventory only hits your profit and loss statement in the year you actually sell it.
Does this change if I also sell to customers in other EU countries? Once your combined cross-border sales to EU consumers pass the €10,000 annual threshold, the OSS scheme comes into play, separately from everything on inventory and payment processors above. Our OSS threshold checker walks through that specific question.
New to running a business in the Netherlands?
If you're setting up an online store here as a founder new to the Dutch system, a lot of this, VAT rates, inventory rules, when a payment processor's payout actually counts as revenue, tends to raise more questions the deeper you get into it. At Sophy &Co. we start helping expat entrepreneurs before the paperwork is even filed, not just once the company already exists. Book a call and we'll walk you through what setting up shop in the Netherlands actually involves.
Our team works across English, Dutch, Italian, Chinese, Spanish, Papiamento, German, and some French and Polish, so you can explain your business in whatever language is easiest. We're a woman-led, diverse team, both women and men, and proudly LGBTQIA-friendly, and we can also point you toward trusted partners, banks, lawyers and notaries if you need them.
How we handle this for you
At Sophy &Co. we turn your inventory records, payment processor exports and sales channels into bookkeeping that actually holds up, even when you're selling through more than one channel at once. Share your purchase invoices and payment processor statements with us, that's really all it takes, we take care of the rest. One flat monthly fee, cancel any time.
Take a look at our e-commerce bookkeeping services, read how it works for Bol.com and Amazon sellers, or check our pricing. Not sure what applies to your situation? Get in touch for a free, no-obligation conversation.
Want the official rules? See the Belastingdienst on VAT and e-commerce, or the KVK for the basic rules on business administration and bookkeeping.