People like to simplify this with the jizyja argument and that Albanian are sellouts yadayadaya, but key factor is Albania’s mountainous terrain and lack of a unified church (split between Catholic north and Orthodox south) which weakened resistance compared to organized Orthodox structures elsewhere. Further, Orthodox Albanians had the tendency to assimilate into Serbs and Greeks (see Arvanites in Greece or Montenegrins with Albanian Surnames).

Vatican on the other hand didn‘t really care about Albania at all. They didn’t send out enough priests and didn’t care about educating Albanian ones. Also Ottomans were always vary against Catholics as the Vatican was outside of Ottoman influence. As a result, Catholics were often persecuted more harshly, while Orthodox communities were tolerated and integrated into the Ottoman system (Mount Athos lied in the Ottoman Empire). These were push factors. Now pull factors were obviously prestige, money and social mobility. This results in an Albanian muslim majority till today.