In this particular example, I don't feel there is any difference in meaning between at and in, but I prefer in with the indefinite article, at with the definite article
So the only difference is the usual difference between the definite and indefinite articles.
We met in a café. <- Some café, undefined.
We met at the café. <- A particular café that speaker and listener understand either because it has just been talked about or because it is a particular café that we know as "the café".