The early history of San Ponso is written almost entirely in a number of stone plaques, including four in white marble, and other monuments of the Gallic tradition, which confirm the early process of Romanization of the area. News about the Lombard period, to which the church dates back, are rather fragmentary, though it is known that a fortified village existed on the heights of Belmonte.

In the Middle Ages, San Ponso followed the destiny of many small towns and was hit by war, poverty and plague. In the sixteenth and seventeenth century it was included in the jurisdiction of Salassa, under the Counts of Valperga; it regained its autonomy as a municipality in 1693, then lost it in 1929, when it was aggregated to Salassa again, until 1947 when it was reinstated as a municipality.