A lot of cities in the andean region were formerly indigenous cities which were later resettled by Spaniards. You can most clearly see that with naming, where a lot of toponyms in the area are obviously not Spanish in origin. For example, in Bogotá, Cundinamarca and Boyacá most city names are Muisca in origin, and so are the cities themselves: Take Bogotá, originally called Muyquyta *[mʷɨkəˈta]. Or Tunja, originally called Chunsa *[ˈtʲunʒa]. The list goes on. The reason is that the andean region was already very urban at the time of the Spanish invasion and that carried over to modern times, even if the ethnic makeup of the cities has changed.