The rest of his reign was also marked by numerous Qizilbāsh rebellions, which Bayezid II tried to overcome by deporting thousands of Qizilbāsh from Anatolia to some of the new conquered coastal areas of Greece: Morea, Modon, Coron and Lepanto.
Resten af hans regeringstid var også præget af en masse qizilbāsh-oprør, som Bayezid II bekæmpede ved at deportere tusindvis af qizilbāsh'er fra Anatolien til nogle nyerobrede kystområder i Grækenland: Morea, Modon, Coron og Lepanto.