I just had a customer experience lots of difficulty in checking out on my website using Afterpay, which has been integrated with my website for well over a year, now. She started by shopping on our store via the Afterpay app on her phone, then entered the checkout, when Shop Pay sent her a code to enter. (Which, of course, she did.) That transitioned her to Shop Pay, where Afterpay was stripped from the payment options. I was able to recreate the issue with her and have to say, it is really confusing from a customerâs perspective. Any thoughts on how this can get resolved?
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 Payâs interfaceâwhere 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:
- Donât enter the Shop Pay verification code when promptedâclose 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 âlater this year,â but merchants continue experiencing the issue with no clear fix.
4 Likes
we have a similar issue- Shop takes over and wonât show all the shipping rates or payment options.
Any help would be great.
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Yes, weâre starting to field complaints from customers experiencing the same issue - did anyone find a solution?
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Unfortunately, no. Itâs not in Shopifyâs interest to get this resolved so they apparently ignored it.
Thanks @Mary_Spinelli , we mightâve figured this out and think itâs because of they way Shop Pay doesnât make it obvious that you can switch from a CC to AfterPay etc.
See the circles in red in the examples attached, if a customers verifies via Shop Pay, they should see either âCardâ or âPaymentâ.
Itâs not obvious but you can tap to change the payment method, then they choose âAlternative Payment Methodsâ then âAfterPayâ (or AMEX, Laybuy, whatever). However, Iâm currently travelling so donât have my usual SIM card in so canât verify with Shop Pay to confirm for myself.
Hope that helps someone. The UI here is not very intuitive which is causing confusion.
Regards, Ben
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Unfortunately, despite assurances from Shopify, the customer we were helping (and made the screenshot for) still couldnât select AfterPay from: Payment > Alternative payment methods.
Have also asked AfterPay so maybe youâre right, Shop Pay does block AfterPay. So frustrating.
When you get to payment. Shop pay will pop up to enter the code sent to your number. Do not enter the code, close the pop up and youâll see other payment options. Such as enter your card, after pay.
Thanks but the main problem is that customers are totally confused - we get regular emails about this now which means many more are simply leaving our site.
Some people donât even think we accept VISA! They think the accelerated checkout buttons (shopay, Apple Pay etc) are the only payment methods we accept.
Shopify told me a new checkout system will launch later this year but in the meantime, customers are getting confused about how to pay. Which seems silly - right?
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Yes, Thatâs correct. As a shop owner, I know to do that. But customers do
not realize that their order is being taken over by ShopPay and they just
follow the instructions and enter the code.
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No, I havenât found a solution yet. I ended up using Shop pay and now when I found this, I realuze I wasnât supposed to do that. I couldnât understand why it just kept showing shop pay inside the after pay app. I really wanted my order, and it was just over $70.00, so I will hopefully find the answer and only use shop pay again of I choose to. It seems wrong that this happened to afterpay.
Iâm having the exact same problem. Itâs creating chaos with customers either leaving our checkout because they cannot figure out how to order via AfterPay or placing orders with ShopPay in error and then ringing us asking for refunds.
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Has anyone found a resolution to this, other than having to explain to customers not to enter the code to sign in to Shop Pay?
Samething happen to me inside the app, but if you click on the 3 dots and open in browser youâll get all the payment options again when you check out
Same issue, three years later, shame on Shopify.
On our site our conversion rate dropped by over 60%.
Removed Shoppay and conversions went back up.
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Yes this is a real problem and really infuriating. I canât get around it at all
Iâm just a person trying to buy things not a shop. Itâs hell
Hi everyone, I have had my website set up like this for 3 years and never realised there was an issue, however the Shop Pay thing kind of automatically added itself ages ago⌠anyway I have now spent hours over many days talking to Shopify and AfterPay about this, it is clearly a Shopify issue.
I am wondering if anyone has tested turning off Shop Pay. I have just done this and seem to be able to see AfterPay again.
I am going to check this each day to see if it helps.
I tried to upload images but it wont accept pngs, basically go to settings in Shopify, payments (on left), manage (top right), manage payment methods (top right), then disable Shop Pay button. This seems to disable the Shop Pay integration but not the actual payments, mine still allows, visa, mastercard, google pay and apple pay.
Hi all I just worked out how to use after pay. You pick the option check out as guest and after pay comes up as a option. You may have to add your address and details again but it works. I ran in with the problem and now it works. Hope this helps.
Use custom cart scripts or checkout to prevent Shop Pay from interfering with Afterpay by disabling accelerated checkouts like Shop Pay for those sessions that come through the Afterpay app. liquid edits. This keeps Afterpay present during the checkout. OR Lead them to shop directly on your store instead of through the Afterpay app. hope this helps