"It's available AT/ON any online store.'

Normally when talking about physical stores we say at/in, but when talking about online stores do we say ON or AT?

Both at and on seem to be in common usage. Go to Fraze dot it, and then search for "at amazon.com" and "on amazon.com". You will find that both forms are commonly used.

Thank you very much. By any chance is 'IN' ever used with online stores?

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I don't think "in" is used with online stores. Again, I checked Fraze.it and did not find any instances of "in".