Can payout fees be deducted from monthly bills instead of payouts?

Topic summary

A user asks whether Shopify can deduct payout fees from monthly bills instead of netting them from payouts, and whether individual per-order payouts are possible instead of batched payouts. Their goal is to align payout amounts with their internal ordering system in QuickBooks.

Current Limitations:

  • Shopify automatically deducts transaction fees directly from payouts with no option to bill them separately
  • Payouts are grouped in batches; per-order payouts are not natively supported

Suggested Workarounds:

  • Integrate Shopify Payments with QuickBooks to track fees separately
  • Use QuickBooks rules or Shopify’s detailed payout reports for reconciliation
  • Consider third-party payment processors that support per-order payouts (though this may incur additional fees)

The discussion remains unresolved as the requested features are not available within Shopify’s current system.

Summarized with AI on October 30. AI used: claude-sonnet-4-5-20250929.

Q: Currently, when I receive a payout from Shopify, the amount is net of fees. Is it possible to have the fees added to the monthly bill instead, so that the payout matches our internal ordering system?

Q: Instead of receiving a single payout for multiple orders in a day, can I request individual payouts per order?

NOTES; I am using quickbooks.

Hi @kamchowdhury

Unfortunately, Shopify deducts transaction fees directly from payouts, and there isn’t an option to have them added to your monthly bill instead. However, you can track fees separately in QuickBooks by integrating it with Shopify Payments to match your internal ordering system more accurately.

Regarding payouts, Shopify groups orders into batch payouts, and there’s no built-in way to receive payouts on a per-order basis. A potential workaround is using a third-party payment processor that supports per-order payouts, but that might come with additional fees.

If keeping records clean is your main concern, consider using QuickBooks rules or Shopify’s detailed payout reports to reconcile transactions more efficiently.