Could and would Apple allow merchants to accept Apple Pay on their websites (not just in the apps)? What are the security issues and potential workarounds?

The Pay infrastructure is based on secure element guidelines.

There are a few factors that are required for the transaction to be valid. One of those is the merchant must have an employee or other designate to be in physical company with the Pay customer, to verify intent to purchase.

Another requirement is to advise the Pay customer of the amount of the transaction,

Finally, they need to authorize the transaction process begin.

On the Pay customer side the requirements are

L  Allow a query for sufficient funding,
2.  Allow location to polled to verify if they are where the merchant scanner is geo-located.
3. Provide biometric security authentication

Since there is no secure element transaction, Pay wouldn’t be used over the web, or in an application unless they are physically at the merchant for verification. There is no app requirement outside of PassBook (which only holds the customer card) for Pay

That’s not to say you wouldn’t be able to use an apple handset to make purchases as a platform for e-comm. using the browser or application in the handset

Pay is a payment system that uses hardware as a solution for the authorization.

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