Shop Pay Hijacks Checkout and Blocks Afterpay as a Payment Option

Shopify Discussion

Topic summary

Core Issue:
Shop Pay intercepts the checkout process when customers shop through the Afterpay app, sending verification codes that redirect users to Shop Pay’s interface—where Afterpay is no longer visible as a payment option.

Customer Impact:

  • Significant confusion leading to abandoned carts and conversion rate drops (one merchant reported over 60% decline)
  • Customers mistakenly believe only accelerated checkout options (Shop Pay, Apple Pay) are accepted
  • Some complete purchases via Shop Pay unintentionally, then request refunds

Attempted Workarounds:

  • Don’t enter the Shop Pay verification code when prompted—close the popup to see other payment methods
  • Afterpay may be accessible under Payment > Alternative Payment Methods, though this UI is not intuitive
  • Checkout as guest to bypass Shop Pay interference
  • Open Afterpay app links in browser (via three-dot menu) instead of in-app
  • Disable Shop Pay button entirely in Shopify settings (Settings > Payments > Manage > Disable Shop Pay button)
  • Use custom Liquid scripts to prevent Shop Pay from activating during Afterpay sessions

Status:
No official resolution after 3+ years. Shopify mentioned a new checkout system launching “later this year,” but merchants continue experiencing the issue with no clear fix.

Summarized with AI on October 26. AI used: claude-sonnet-4-5-20250929.
6

Unfortunately, despite assurances from Shopify, the customer we were helping (and made the screenshot for) still couldn’t select AfterPay from: Payment > Alternative payment methods.

Have also asked AfterPay so maybe you’re right, Shop Pay does block AfterPay. So frustrating.