Cinciano is probably Roman in origin, and may have belonged to the Gens Cincia. In 1126 it was gifted by Zaballina, widow of Ridolfino da Catignano, to Gotifredo, Bishop of Florence, along with the castles of Linari and Catignano. It is also mentioned in documents from 1292, when some lands were rented by Bishop Andrea for the annual fee of 14 bushels of wheat.
The springs and the bathing area are documented from the 13th century. Due to its commanding position overlooking the Elsa valley and proximity to the ancient Poggio di Bonizio (named after local nobleman Bonizio Segni), strategically positioned on the Via Francigena, Cinciano followed the alternating fortunes and events of the area until it was annexed by the Florentine Republic.
Throughout most of the 12th century the area was a bone of contention between the bishops of Florence and Siena, who both claimed ownership. During the 13th century, when Poggibonsi continued to favour the Empire against Guelph Florence, it suffered the first blow in a conflict that led to Charles of Anjou’s occupation of the area and subsequent destruction of old Poggibonsi.