This was originally posted in the Square seller forums, but was advised to post it here instead.
When we setup Apple Pay in the Square POS app on an iPhone the merchant ID doesn’t seem to get sent to Apple. When we go to Apple Business Connect it says:
“You need a merchant ID from your payment service provider”.
We are also working with Apple support and as part of the process they sent us this link that allows you to sign in with an Apple Account and unlink any associated merchant IDs so that you can try re-registering.
https://businessconnect.apple.com/taptopay/removeall
Does anyone know how we can get Apple Pay through Square to connect to Apple Business Connect?
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Based on the information you’ve provided, the following documentation will help answer your question:
Additional Documentation
Payment API: Process Online and In-Person Payments
Build on iOS: Point of Sale API
Square Developer Documentation
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If this is with Apple Pay within the Square app’s Apple Pay Square is the merchant of record since the app is using Square’s implementation of Apple Pay. Individual merchant_ids for Square accounts aren’t passed to Apple. 
When I use the link I provided above, I see that there is a Square merchant ID associated with our Apple account. It just isn’t showing in the Apple Business Connect portal.
I believe that merchant_id is for building application that accept Apple Pay. For example if a developer build an integration with our In-App Payments SDK and wanted to enable Apple Pay on iOS devices.
I’m not really familiar with Apple Business Connect but the merchant ID that your showing is for app development from what I’m aware of.
