E-commerce Bookkeeping: The Complete Guide for Online Sellers
From invoice management to VAT returns, here's everything you need to know about keeping your books clean as a marketplace seller.
Bookkeeping isn't the most exciting part of running an e-commerce business, but get it wrong and you'll face fines, missed deductions, or worse — a tax audit. Here's how to stay on top of it.
The basics: what you need to track
As an online seller, your bookkeeping needs to cover:
- Sales invoices — Every sale needs a compliant invoice, whether B2B or B2C
- Purchase invoices — Everything you buy for your business (inventory, shipping materials, software)
- Bank transactions — Match every payment to an invoice
- VAT records — Track VAT collected and paid, broken down by rate
- Marketplace payouts — Reconcile what the marketplace paid you vs. what you actually sold
The marketplace payout trap
One of the biggest mistakes new sellers make is booking marketplace payouts as revenue. A payout from Bol.com is not your revenue — it's your revenue minus their commission, minus shipping costs, minus returns. You need to book the gross sale, then separately book the fees and commissions as expenses.
Invoice numbering
Tax authorities require sequential invoice numbering. This means no gaps: INV-001, INV-002, INV-003. If you void an invoice, it should still exist in your records — just marked as voided. Automatic invoicing tools handle this for you, but if you're doing it manually, be disciplined about it.
VAT rates in the Netherlands
The standard VAT rate is 21%. The reduced rate (9%) applies to specific categories like food, books, and medicines. The zero rate (0%) applies to exports within the EU to VAT-registered businesses (reverse charge). Make sure your invoicing matches the correct rate for each product.
When to get an accountant
If you're doing more than €50,000 in revenue, it's worth hiring a bookkeeper. Below that, tools like Moneybird or e-Boekhouden combined with automatic invoicing can handle most of what you need. The key is consistency — update your books weekly, not once a year before tax season.
Automation is your friend
The fewer manual steps in your bookkeeping, the fewer errors you'll make. Automatic invoicing eliminates the biggest manual step for most sellers. Combine it with bank feed integration in your accounting software, and you've eliminated 80% of the busywork.
