Orders appear paid in Shopify, but corresponding charges are missing from Stripe, totaling roughly €4,000 over several months.
Timeline/trigger: The issue began around July 14, coinciding with Shopify’s payment provider label changing from “Stripe” to “Stripe Card Payments” (Stripe as the payment gateway within Shopify).
Actions so far: The merchant reconnected Stripe and Shopify on Dec 12. New payments now process and appear in Stripe, but historical payments from the affected period remain absent.
Vendor responses: Stripe reports no issues on their end and says they have not been contacted by Shopify about this case. Shopify support states the matter is “under investigation,” but has provided no concrete updates and has gone silent for several days.
Impact/concern: Significant funds may be unrecoverable without intervention; root cause likely tied to the provider transition.
Ask: Seeking others with similar experiences and advice on effective escalation.
Status: Unresolved and ongoing. Key unknowns: whether missing funds can be recovered and the exact failure point during the provider change.
Summarized with AI on December 16.
AI used: gpt-5.
Hi everyone, has anyone experienced a serious issue between Shopify and Stripe like this?
Since around July 14, orders in Shopify are created normally and customers successfully pay, but the payments do not appear in the Stripe dashboard at all. This affects several months of orders, with approximately €4,000 missing in Stripe.
Around the same time, the payment provider in Shopify changed from “Stripe” to “Stripe Card Payments”, and this is exactly when the issue started. After reconnecting Stripe and Shopify on December 12, new payments are working again, but the historical payments are still missing.
Stripe claims that everything is fine on their side and that they have not been contacted by Shopify regarding my case. Shopify support, on the other hand, keeps saying that the issue is “under investigation,” but there has been no progress and no concrete updates, and I’ve now been without a response for several days.
Honestly, I’m worried that we may never recover these funds, so I wanted to ask:
Has anyone encountered a similar situation?
Or do you have any advice on how to escalate this effectively so it actually gets resolved?
That sounds really stressful. A few key things to clarify first: were these orders paid via Shopify Payments or via a custom Stripe integration, and do the orders show a successful charge ID or transaction reference inside the Shopify order timeline? Also, during the switch from “Stripe” to “Stripe Card Payments,” did Shopify migrate the payment app automatically or was there a manual reconnect or app replacement involved?
From experience, when payments show as paid in Shopify but never appear in Stripe, it often points to a disconnected or replaced Stripe account, test mode vs live mode mismatch, or charges being routed to a different Stripe account created during the provider change. I would strongly recommend asking Shopify support for the exact Stripe account ID used before and after July 14, and requesting a payment export with gateway transaction IDs, then giving those IDs directly to Stripe support for tracing. On the Shopify side, push for escalation to their payments or partnerships team and ask for written confirmation of where the funds are currently held, if anywhere.
For the future, many merchants avoid this kind of opaque handoff by using a third-party Shopify Stripe Checkout like Easy||Pie Checkout, which connects directly to your own Stripe account, keeps full visibility in the Stripe dashboard, and reduces the risk of payments “disappearing” during Shopify-side provider changes.
This can happen when the payment gateway changes or reconnects. Older payments may be linked to the previous Stripe connection or a different payout account. Check Shopify Payments transaction details and match order IDs. Ask Shopify support to escalate the case to the Payments or Finance team and request written confirmation from Stripe.