I just chatted with Shopify support about this. I had a client place a large order on 6/4 and then on 6/5 she went back to the website and the items were still in her cart. So this made her think the order did not go through so she ordered a second time. She contacted me later that day and told me what happened and asked if she had actually ordered twice, and she had. Now I normally will take the fees from the customers end as this is one of our shop policies if you pay using Shopify Pay. But this was not the fault of my client but instead a glitch in the Shopify system. During the chat the agent admitted twice it was their fault (see screen shot) but they still would not refund me. There should be some sort of exception here. If the order was triggered by a system glitch that is not my fault or my customers why should we be responsible for the fees incurred. I can see a Class Action Lawsuit here. I mean Shopify can cause thousands of glitches in a day and make a fee from each one. Sounds super shady.
Topic summary
Merchants report being charged non‑refundable fees (often around 2% processing/gateway fees) even when orders are cancelled or refunded, leading to monthly losses and large one‑off costs.
Shopify staff clarify a policy change: since March 2020 (US) and January 2021 (other regions), Shopify Payments does not refund the original processing fee on refunds (per Terms of Service 5.10). They state Shopify incurs costs to process refunds and does not charge an additional fee on the refund itself.
Staff add most major gateways also keep fees, linking to documentation for PayPal, Square, Authorize.net, Stripe, 2Checkout, and Affirm. Merchants counter that immediate refunds still incur fees, cross‑border currency conversion fees aren’t returned, and request a 12–24h grace period; some raise legal concerns.
A duplicate‑order case is attributed by staff to theme/cart behavior (cached carts, multi‑device logins, or custom code), advising theme developer support; a screenshot is referenced.
Suggested mitigation: consider manual capture (authorize then capture) to verify orders before funds are captured, and reduce refund causes. Status: no policy change; feedback will be forwarded. No gateway that refunds fees on refunds was identified; discussion remains open.
