When?

I presume you mean the Byzantine Empire in general or Constantinople in particular. Depends on whether you were a war prisoner (confinement, but allowed to pray), a member of the merchant class (privileges, including the right to trade, a separate neighbourhood and a mosque, and at least since the Palaiologan period, a qadi/muslim judge to rule on cases involving muslims) or a sailor stranded on Byzantine shores (depends on the goodwill of the locals). In general (and in times of peace) tolerated and traded with.