Major increase of conversions from direct traffic after use of Shopify Payments

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Topic summary

Main issue: After switching from Mollie to Shopify Payments, a sharp rise in conversions attributed to direct/none (~5% to ~50%) appears in Google Analytics. Many conversions show landing pages like /checkout/processing with very short sessions, suggesting source is lost during the payment flow.

Investigation steps and findings:

  • Segments/User Explorer confirm checkout as first page and too-short durations to reflect real sessions.
  • Referrals via hooks.stripe.com; excluding it increases direct attribution.
  • Possible cross-domain tracking lapse (GA client ID handoff, 2-minute window). Attempts to use GA linker in Additional GA JS were tested but inconclusive; Shopify can’t assist on cross-domain parameters.
  • GA4 considered/tried; no native Shopify integration and poor implementations reported; some see the issue worsen in GA4.
  • GTM is the favored fix but effectively limited to Shopify Plus; third-party apps (e.g., Elevar) suggested.

Additional causes/notes:

  • Apple Pay/Google Pay and cookie consent (GDPR) apps can break attribution; GTM + Cookiebot on Shopify Plus mitigates the issue. Residual direct may come from in-app browser switches, cart emails without UTMs, or misconfigured gateways.

Status: Unresolved for non-Plus stores. Shopify acknowledges the issue but has had it “under investigation” for 6+ months with no fix or clear guidance.

Summarized with AI on February 2. AI used: gpt-5.
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Shopify is still looking into it. It’s strange that it’s not a problem with Mollie but it is with Shopify payments. So it looks like Shopify can make some improvements here.

I don’t know about your suggestion, I don’t think we can add it ourselves right?

As soon as I have a solution I will post it here.