The first settlers on the peninsula saw their dreams of riches dashed by the poor soil and pinned their hopes for material improvement on the favors the king would grant them for their work with the region's indigenous people. Mérida emerged from the ancient stones of the Mayan city.

The Order of St. Francis arrived in Yucatán in 1545 to found the Convento Grande de San Francisco, from where they dominated evangelization efforts for three centuries. The southern block of the Main Square was designated as the home of the conquistador, the northern block as the seat of the Royal Houses, representatives of the civil power of the crown, and the eastern block for the construction of the Cathedral and the bishop's house: the Episcopal Palace.