A possible reason was the attacks on them by crusaders and mongols around the 11th and 12th centuries. Another reason could have been the Arab rulers removing taxes from non Muslims and doing other things that hurt there income.
I’m not 100% sure but The Hispanics had more supplies the natives where still fighting with bows and arrows and other things that they made. The Spanish had guns and swords. So it wasent a equal balance between the two sides.
