The origins of the complex are still shrouded in mystery. One of the most famous traditions traces the construction of the abbey to the eighth century, when Prospero, bishop of Tarragona fleeing Spain invaded by the Arabs, chose the bay to shelter and build a church where the relics of the martyr Fruttuoso. The cult of the saint soon spread throughout Liguria, so much so that it attributed special protection functions for sailors.

Much of the Abbey dates back to the X-XI century. In the new structure, the Byzantine dome, built in the tenth century at a perennial spring, was incorporated in the octagonal tower. In this period, the complex of Capodimonte increased its prestige up to assume jurisdiction over the entire promontory of Portofino.

From the thirteenth century the fortunes of San Fruttuoso became intertwined with that of the Doria family, who commissioned the renovation of the building, by building the abbey overlooking the sea with loggia with two orders of three-mullioned windows. In recognition of the many restoration projects promoted by the Doria, the monks allowed them the adjoining crypt on the lower cloister as graveyard family: even today the tombs of white marble and gray stone are visible, dating between 1275 and 1305.

Legend has it that a priest Justin, one of the young men who accompanied San Prospero in his flight from Spain to Liguria, brought with him the ashes of the three martyrs: Fruttuoso bishop and his Deacons Eulogio and Augurio. While sailing in Giustino appeared in a dream the angel of the Lord (in other versions San Fruttuoso itself) revealing that would take them in a overhung place to a great mountain. In a cave of this mountain, he said the angel, lived an enormous dragon, that they should not fear, because, thanks to the powers of the three martyrs, could have cast it out Justin himself. The angel still indicated that under a rock would find a source of water to which they would have had to build a church. The "famous Dragon" is a widespread legend among sailors, perhaps to ward off possible contenders who wanted to get water in the place.

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