Shopify Payments consolidates all card and wallet payments, deducts fees and sends a collective payout to your bank account. For bookkeeping, however, you need gross sales, fees, refunds and payment dates separately - otherwise the EÜR, P&L and VAT will not be correct.
- Shop turnover ≠ bank turnover (fees/refunds missing)
- Fees not separated → Net sales too high
- Refunds do not appear in the VAT
- CSV opens incorrectly in Excel (comma/US date)
- Shopify Admin → Payments → Payouts → Export.
- Export balance transactions (CSV) per payout or period.
- Open CSV in Excel/Sheets correctly with UTF-8, comma/semicolon.
- Map fees/refunds to your own accounts (SKR03/04).
- Optional: Convert PDF payouts to DATEV-CSV/EXTF with KontoCSV.
This is how Shopify Payments payouts work
Every order generates transactions (batch, fees, refund if necessary). These end up in the Shopify Payments balance (“Balance”). At intervals, Shopify combines the due transactions into one payout. There you can see gross sales, fees, refunds/chargebacks and the net amount that goes to the bank account.
Shopify reports often use the sales date (when the purchase occurs). Payouts use the payout date (when the money goes into the bank account). If you only post the bank statement, there are no fees and refunds - the net sales will be too high. Solution: Export transaction/payout reports as CSV and map them cleanly.
Export options in Shopify
Path: Shopify Admin → Settings → Payments → Shopify Payments → View payouts → View transactions → Export.
Includes payout date, transaction type (charge, refund, fee, adjustment), gross, fee, net, currency, references.
Basis for booking separately for fees and refunds.
Reports such as “Payments” or “Finances summary” provide aggregated information on payments, fees and refunds per period.
Good for monthly reconciliation, but the payout CSV is more precise for bank bookings.
Subscription, app or shipping fees are separate invoices and are not part of the Shopify Payments payouts.
Export this CSV separately; they do not replace payout export.
Bank PDF with “SHOPIFY PAYMENTS ...” or PDF from Shopify/email.
Cannot be imported with on-board tools – KontoCSV converts PDF → CSV/DATEV.
Step-by-step: Withdrawal CSV
- Open Shopify Admin → Settings → Payments → Shopify Payments.
- Up View payouts click, select payout.
- View transactions open.
- Top right Export → Balance transactions → Select time period (payout or date range).
- format CSV select, download file (for large periods by email).
- Check columns: Payout Date, Transaction Type, Gross, Fee, Net, Currency, Order/Payout ID.
Open CSV correctly in Excel/Sheets
To ensure that the date and amount formats are correct, do not open CSV by double-clicking:
- Excel → Data → From Text/CSV → File origin UTF-8.
- Select a separator (Shopify usually a comma; for DATEV a semicolon often makes sense later).
- Set column format: Date on DD.MM.YYYY, amounts as a number with a comma and 2 decimal places.
- Optional: Keep the shop ID or payout ID as an additional column if several shops exist.
PDF payouts with KontoCSV
If you only have PDF receipts, you can turn them into CSV or a DATEV EXTF file in seconds:
1. Upload PDF
E.g. upload “Shopify Payments Payout 2025-01-31.pdf” to KontoCSV.
2. Select export profile
Predefined: DATEV, Lexware, Excel – or your own mapping profile.
3. Check & export
Check gross, fee, refunds separately, then export CSV/EXTF.
Fees, refunds & taxes folders
SKR03: 4400 (19%), 8300 (7%), 4970 fees
SKR04: 8400 (19%), 8336 (7%), 6825 fees
OSS/third country: separate revenue account per country/tax rate.
Post refunds as negative sales with correct VAT.
Date (payment date for bank reconciliation)
Gross, fee, net separately
Transaction type (charge, refund, fee, adjustment)
Tax rate/tax amount, currency, order/payout ID
Store account/BU key per type (configurable in KontoCSV).
Import into DATEV & other tools
- DATEV Batch processing expects an EXTF-CSV (file name e.g.
EXTF_ShopifyPayments_2025-01.csv). - Semicolon as separator, date DD.MM.YYYY, check general ledger account length & chart of accounts (SKR03/04).
- Other systems (Lexware, BuchhaltungsButler, sevDesk etc.) accept DATEV-CSV or their own layouts - KontoCSV can generate both.
- For collective payouts, secure the individual transactions as receipts; Store the payout PDF in an audit-proof manner.
Common Problems & Solutions
FAQ
Authoritative links
Conclusion
If you use the payout CSV or convert PDFs via KontoCSV, you will receive a clean database: sales, fees and refunds are separate, match the bank account and can be imported into DATEV without any rework. Result: fewer questions from the tax advisor and a stress-free monthly closing.