San Miniato sits at an historically strategic location atop three small hills where it dominates the lower Arno valley between the valleys of Egola and Elsa. It used to carry the additional sobriquet al Tedesco ("[to] the German") to distinguish it from the convent of San Miniato al Monte in Florence, which is about 40 kilometres (25mi) to the northeast.
In medieval times, San Miniato was on the via Francigena, which was the main connecting route between northern Europe and Rome. It also sits at the intersection of the Florence-Pisa and the Lucca-Siena roads. Over the centuries San Miniato was therefore exposed to a constant flow of friendly and hostile armies, traders in all manner of goods and services, and other travelers from near and far.
Archaeological evidence indicates that the site of the city and surrounding area has been settled since at least the paleolithic era. It would have been well known to the Etruscans, and certainly to the Romans, for whom it was a military post called "Quarto".