If you run a Shopify store, you receive regular payouts from your payment provider, whether that is Mollie, Stripe, or PayPal. On the surface this seems straightforward, but the bookkeeping behind each payout is more complex than it looks. Every payout contains transaction fees, sometimes currency conversions, and the question of how to correctly record those fees is one that many store owners get wrong.
Why Payouts and Fees Must Be Booked Separately
When a customer pays €100 through Stripe, you do not receive €100 in your bank account. Stripe deducts transaction fees, for example 1.4% plus €0.25. Your actual payout is €98.35. If you only book that net amount, your bookkeeping is incorrect: your revenue is €100, but you only received €98.35. The difference is a business expense, specifically the payment provider fee.
This might seem like a minor detail, but it adds up quickly. A webshop with €30,000 in monthly revenue and an average Stripe fee of 1.8% is paying over €500 per month in transaction costs. Annually, that is more than €6,000. If you do not book those costs correctly, you present a distorted picture of your profit margin and may end up paying more tax than necessary.
How Shopify and Your Payment Provider Structure a Payout
Shopify works with payment providers like Mollie, Stripe, and PayPal to process payments. Depending on your setup, the process works as follows: a customer pays at checkout, the payment provider processes the transaction and deducts fees, and after a payout period (typically daily or weekly) the net amount is transferred to your bank account.
Each payout therefore consists of multiple layers. There is the gross revenue from all orders in the payout period, minus transaction fees per order, minus any returns or chargebacks, minus other provider-specific charges. Some providers like Stripe send detailed reports per payout. Others like PayPal bundle everything into a less transparent settlement statement.
To process this correctly in Moneybird, you need that detailed breakdown. Without an automated integration, you have to manually look up transactions for each payout period, calculate fees, and select the right ledger accounts. For a deep dive into how to handle payments in Moneybird, read our article on payment reconciliation for Shopify and Moneybird.
The Right Ledger Accounts for Transaction Fees
For correct processing in Moneybird you need at least three types of ledger accounts related to payouts and fees. First, the bank account where payouts arrive. Second, a clearing account for payments in transit, sometimes called a “payments pending” or “bridge account.” Third, an expense account for payment provider fees, for example “Transaction costs payment providers.”
The clearing account is essential because there is often a time gap between when a customer pays and when the payout actually arrives. A customer pays on Monday, but the payout only lands on Thursday. If you book every customer payment directly to your bank account, your bank balance in Moneybird will not match your actual balance. The clearing account bridges this gap.
When creating the expense account for fees, it is advisable to keep a separate account per provider. This lets you easily compare at year end how much you are paying to Mollie, Stripe, and PayPal, and make informed decisions about your payment strategy. For guidance on setting up your chart of accounts, see our article on ledger accounts for Shopify and Moneybird.
VAT on Transaction Fees: Deductible or Not?
A common question is whether the transaction fees charged by payment providers include VAT that you can reclaim. The answer differs by provider and situation. Mollie is a Dutch payment service provider and charges Dutch VAT on its fees. If you are VAT-registered, you can deduct the VAT on Mollie fees as input tax in your return.
Stripe is based in Ireland. Under European VAT rules for B2B services, the reverse charge mechanism applies: the VAT is shifted to you as the recipient in the Netherlands. This means you report the VAT yourself in your VAT return, both as output tax and as input tax. The net effect is zero, but you still need to report it correctly.
PayPal is more complex. PayPal’s fees are in some cases exempt from VAT as a financial service provider. In practice, this means you cannot reclaim VAT on PayPal fees. Always check the invoices from your payment provider to see which VAT regime applies and book the fees using the correct VAT code.
How to Reconcile a Payout in Moneybird
Reconciliation means matching the payout in your bank account to the underlying transactions in your bookkeeping. A correct reconciliation ensures that your bank balance in Moneybird matches your actual bank account and that all revenue and costs are on the right accounts.
A typical payout reconciliation in Moneybird works in steps. First, book the gross revenue for the payout period to the clearing account. Then book the transaction fees as an expense to the fees account. Then book any returns as a correction to revenue. Finally, the net payout in your bank account matches the balance on the clearing account, bringing it to zero.
Doing this manually takes at least thirty minutes per payout. With daily payouts, that is more than ten hours per month spent purely on reconciling payment provider fees. That is time better spent running your store.
Automating the Process with Schakel
Schakel does not only pull orders from Shopify, it also processes the related payment information. The app links each payment to the correct invoice in Moneybird and ensures accurate representation of amounts received. This gives you a real-time view of outstanding receivables and payments collected.
With automatic synchronization, you always know which invoices are still outstanding and which have been paid. You no longer need to manually scroll through Shopify reports to check whether a payment has come in. Schakel automatically tracks the status of each invoice based on the information Shopify sends through.
Transaction fees themselves are most efficiently processed using the payout report from your payment provider. By importing this report periodically, you can book all fees at once rather than transaction by transaction. This saves time and reduces the risk of errors. To learn more about automating your entire Shopify bookkeeping workflow, read our article on automating Shopify accounting with Moneybird.
A Practical Step-by-Step Plan for Store Owners
If you are currently processing payouts and transaction fees manually, it is worth reviewing your workflow. Start by creating the right ledger accounts in Moneybird if you have not already: a clearing account per payment provider and an expense account for fees. Then check the VAT status of each payment provider you use and configure the correct VAT codes on the expense accounts.
Next, use the payout reports from your payment providers as the basis for monthly reconciliation. Mollie, Stripe, and PayPal all offer export options in CSV or Excel. By processing these reports systematically, you keep your bookkeeping current and significantly reduce the workload at your quarterly close.
Finally, consider an automated integration for your invoice processing. Schakel ensures that your orders automatically appear as invoices in Moneybird, so you can focus your energy on reconciling payouts and fees rather than manual invoice entry. With that time saving, you can keep your administration properly up to date on an ongoing basis.
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