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. Repeat that mistake across a month of payouts and your books conceal both the sales and the cost of collecting them.
This simplified example assumes the €100 is entirely sales, with no tax or other adjustments. The €3 is an illustrative fee, not a quoted Shopify rate.
LedgerLeaf Pro helps you build the entry from payout records inside Shopify admin. You review the payment activity, export the supporting data, and prepare the sales file beside it. Your accountant gets an explained deposit rather than another number to investigate.
Why the bank feed and native reports leave work unfinished
A bank feed shows the €97 that arrived. It cannot tell you how much Shopify deducted or what the customer payment included.
Shopify does provide fees in its payout transaction records. The weakness is the preparation around those records. Its payout details, sales reports, and bank deposits serve different purposes. You still have to assemble them into a useful accounting handoff. A homemade workbook adds another place to mix dates, overwrite formulas, or count the same fee twice.
LedgerLeaf puts payout reporting and customisable sales exports in one app. Preparing the records is easier because you stay in Shopify admin, with no separate external account and no need to rebuild the sales spreadsheet each month.
Prepare the fee evidence in LedgerLeaf
Start with one bank deposit
Open Payouts in LedgerLeaf Pro and review the Shopify Payments activity for the deposit you are checking. Export the payout data and keep the payout reference, currency, and date with your bank note. Record the bank receipt date separately if the transfer arrived later.
For our example, use the exported records to prepare this breakdown for your accountant.
| Activity behind the deposit | Amount | Accounting purpose |
|---|---|---|
| Customer payment | €100 | Gross payment to allocate |
| Processing fee | €3 deducted | Separate processing expense |
| Net payout | €97 | Bank transfer to match |
Use the reported fee rather than calling every sales-to-bank difference a processing cost. Suppose the payout also includes a €20 refund and the reported fee remains €3. The bank receives €77. Booking the €23 difference as fees would hide the refund and overstate processing costs by €20.
Add the sales evidence in the same app
Open Sales and prepare a CSV or XLSX export for the relevant orders. Include the order reference, payment, refund, and tax information your accountant needs, then save that column selection as a preset.
Keep the sales file with the payout export. It helps your accountant allocate the customer payment between revenue and any tax collected. The payout file explains the fee and cash movement. Their dates and totals can differ, so the sales export should not be forced to match the bank deposit.
Next month, reuse the sales preset and prepare the new payout records. That removes repeated column cleanup while retaining the explanation behind each fee entry.
Use those records to explain the journal entry
A common approach uses a Shopify Payments clearing account between the customer payment and the bank. For the simplified €100 example, the records prepared above support these entries.
| 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 and releases €3 to processing expense and €97 to the bank. It returns to zero for this fully paid activity. Match the bank deposit against that transfer rather than booking another sale or deducting the fee again.
Real entries need the correct allocation for taxes, refunds, and other adjustments. Agree the accounts and timing with your accountant. LedgerLeaf supplies the supporting Shopify records for that decision.
Keep month-end differences explainable
Shopify’s Payments activity report describes balance movements rather than accounting revenue. Payout timing, reserves, pending activity, or currency differences can leave a legitimate clearing balance. Keep those items with the LedgerLeaf export and carry an explained balance forward instead of changing sales to force it to zero.
Keep Shopify subscription and app bills, and third-party gateway statements, separate. If tax applies to processing fees, retain the relevant tax documentation and confirm its treatment with your accountant.
Pay for the preparation you need
A2X’s Shopify Mini plan costs US$29 a month for up to 200 orders and connects payout summaries to accounting software. For a merchant who needs files for an accountant, that means a higher bill and another accounting connection to manage.
LedgerLeaf Pro costs US$5.90 a month. Its payout reporting and reusable sales exports make it the simpler, better-value choice for this handoff. Prices checked on 11 October 2026.
Try LedgerLeaf Pro’s seven-day trial and prepare the records behind one bank deposit before your next accountant handoff.
