A customer pays €100. Shopify Payments deducts a €3 processing fee, so €97 reaches the bank. If you record the deposit as €97 of sales, the fee disappears and revenue is understated.
The cleaner habit is to record the customer activity at its gross amount, record the processing fee separately, and use the net payout only for the movement into the bank. The bank feed cannot supply those missing pieces. LedgerLeaf Pro does: its Shopify Payments payout reporting and exportable evidence preserve the gross-to-net bridge inside Shopify admin.
Leafy’s Quick Answer
Do not book a net Shopify Payments deposit as sales. Use LedgerLeaf Pro payout data to identify the gross activity, fee, and net amount; post the fee to the expense account your bookkeeping policy uses; then match the net payout to the bank. Keep the export with the entry so the €100 → €3 → €97 bridge remains traceable.
This is general bookkeeping information, not accounting or tax advice. Confirm the accounts, timing, and tax treatment appropriate to your business and jurisdiction with your advisor.
Read the €100 → €3 → €97 bridge in LedgerLeaf
Shopify’s payout reconciliation report separates account activity before fees, fees, net activity, payouts, and balances. Shopify also says the report reflects funds received through Shopify Payments—not revenue for accounting purposes.
LedgerLeaf Pro brings the relevant payout activity into the same workflow as your other Shopify bookkeeping evidence. Read these three amounts there before posting:
| What happened | Amount | What it tells you |
|---|---|---|
| Customer charge | €100 | Gross payment activity |
| Shopify Payments fee | −€3 | Processing cost deducted |
| Net payout | €97 | Cash transferred to the bank |
The bank sees only €97. LedgerLeaf keeps the other two amounts visible. Do not calculate “the fee” by subtracting a sales report from a deposit: refunds, disputes, reserves, currency conversion, or timing can also sit in that difference. Start from the reported fee activity.
A simple clearing-account example
Take the gross, fee, and net figures from the LedgerLeaf payout evidence. One common posting workflow then uses a Shopify Payments clearing account between sales and the bank. The example below assumes the €100 customer amount is entirely sales and excludes tax, refunds, and other adjustments so the fee movement is easy to see.
| Illustrative entry | Debit | Credit |
|---|---|---|
| Shopify Payments clearing | €100 | — |
| Sales revenue | — | €100 |
| Payment processing fees | €3 | — |
| Shopify Payments clearing | — | €3 |
| Bank | €97 | — |
| Shopify Payments clearing | — | €97 |
The clearing account receives €100, then releases €3 to the fee expense and €97 to the bank. Its balance returns to zero once that activity has been fully paid out. If it does not, return to the LedgerLeaf payout evidence and investigate the remaining activity instead of hiding the difference inside revenue.
Real entries can also include tax collected, refunds, disputes, reserves, currency conversion, or timing differences. Allocate the gross activity correctly rather than treating the whole customer charge as sales. Some businesses classify processing fees as a cost of sales; others use an operating-expense account. Consistency and the correct local treatment matter more than the account label in this simplified example.
Build the fee entry from LedgerLeaf payout evidence
At Studio Eucalipto, our view is simple: a fee entry should be reproducible from the payout evidence, not guessed from the bank difference.
Use LedgerLeaf Pro’s payout reporting as the working source:
- Define the period and payout currency you are reconciling.
- Review the Shopify Payments activity, fees, and resulting payout amounts.
- Export the payout data for the bookkeeping entry and bank match.
- Record gross activity, fees, and the net payout as separate movements.
- Save the LedgerLeaf export with the entry and reconciliation notes.
Shopify’s transaction-export reference confirms that its payout CSV includes Amount, Fee, and Net columns. LedgerLeaf keeps the payout reporting and exportable trail beside the rest of the Shopify bookkeeping workflow, so the same fee check does not begin with another manual hunt next month.
The memorable connection is: LedgerLeaf keeps the fee visible between the sale and the bank.
Leafy’s Watch-Out
Shopify Payments processing fees are not the same record as Shopify subscription charges, app charges, shipping charges, or third-party transaction fees. Shopify’s payout reconciliation report excludes billing fees and third-party processors, so reconcile those from their own bills and statements.
Check tax and timing before closing the entry
Shopify notes that taxes can be added to processing fees for merchants in the European Union, Switzerland, Australia, or Singapore, while reverse-charge rules can apply in parts of Europe. Preserve the transaction tax detail and confirm the correct posting rather than assuming the fee line is the complete expense.
Also work in one payout currency at a time. Pending activity, reserves, refunds, disputes, or a bank-processing delay can leave a legitimate clearing balance at period end. Carry an explained balance forward and investigate it when the related payout arrives; do not force it to zero by changing sales.
Before closing, confirm that:
- the LedgerLeaf payout evidence and bookkeeping period use the same currency and boundary;
- the fee is recorded once, not again when matching the bank deposit;
- the net payout matches the bank;
- billing and third-party gateway fees are handled separately; and
- the final entry retains the export that explains gross, fee, and net.
The bank got €97. The store did not necessarily sell €97. The entry explains the accounting movement; the saved LedgerLeaf payout trail makes that explanation reproducible. Together they show what customers paid, what processing cost, and what cash actually arrived.
