Blog · 15 October 2026 · approx. 5 min read

Reconciling PayPal properly: why accountants struggle – and how to make it easier

Monday morning, bank statement: “PayPal Europe S.à r.l. – €1,483.17”. One single line. For the shop, that’s 14 orders from three countries, two refunds and one purchase in Swiss francs. For the accountant, it’s a puzzle. This is where the PayPal problem begins.

Why PayPal is so hard to reconcile

With a normal bank transfer it’s simple: one customer, one amount, one reference. PayPal works differently. It’s more like a separate account between customer and bank – with its own rules. Five things make reconciliation painful:

1. Fees are deducted immediately

A customer pays €100.00 and, for example, €96.76 arrives in the PayPal account. The fee is withheld right away. In the books, however, you need the full revenue (€100.00) and the fee (€3.24) separately. If you only see net amounts, revenue is understated – and the fee is missing as an expense.

2. One payout = many orders

The money first stays in PayPal and is transferred to the bank in bulk – manually or automatically. The bank statement then shows one amount without order numbers. Which payments are inside is only visible in the PayPal account itself.

3. Currency conversion

When a customer pays in CHF, GBP or USD, PayPal converts – at its own rate, which often includes a markup. The converted amount then matches neither the order value in foreign currency nor the daily rate. The difference has to go somewhere.

4. Refunds, partial refunds, buyer protection

Refunds are netted against later payments. In buyer-protection cases, money is held or reversed. A payout can therefore be smaller than the sum of sales – without this being visible on the bank statement.

5. Timing

Order in September, payout in October: without clean matching, revenue ends up in the wrong month – awkward for VAT returns.

An example

The bank statement only shows the last line. Everything above it has to be pieced together.

How to do it properly

Many accountants recommend treating PayPal as a separate bank account in the books: every payment, fee and refund is booked there individually, and the payout becomes a simple transfer between PayPal and the bank. That requires the full PayPal transaction list – and someone who matches every line to the right order. That’s exactly what takes time.

How to apply this in your case is best clarified with your tax advisor – this article is not tax advice.

What ZentryaHub is built to take over

ZentryaHub already matches bank receipts to orders and invoices automatically today (for example 3S Money, Wio and CSV statements). PayPal reconciliation is in development and is designed to handle exactly the steps above:

• match every PayPal payment to the right order,
• show gross revenue, fee and exchange rate separately,
• link refunds to the original order,
• break a bundled payout down into its individual orders,
• hand everything cleanly to accounting (Odoo today, other systems on request).

The goal: the question “What’s inside the €1,483.17?” gets answered in one click – for you and for your accountant.