In written documents, Bibinje is first mentioned in 1214. The area of Bibinje has been inhabited since Roman times which is evidenced by the origins of the name Bibinje. It was named after Vibius the Roman patrician who owned property on the territory of present Bibinje.

According to a folk tale, the place was originally built on the top of the hill above the present location (more precisely, in the field of Bibinje, on the slopes of the hill). Today, the centre of that locality is called Petrina after the small church of Saint Peter from the 8th century. Due to the plague raging at that time, people moved from Petrina to the present location on the peninsula by the sea.

By the establishment of the Benedictines Order in Zadar in 1066, Croatian King Petar Krešimir IV gave the royal property Točinja (today Bibinje) to the Order of Benedictines as a gift to keep in permanent possession. Under the protection of Benedictines, from the late middle Ages until the first Turkish invasion, Bibinje experiences envious economic development.

In the middle of the 15th century, Turkish invasions into the region begin, which remains one of the most difficult periods in its entire history. One of the greatest folk heroes from the struggle era against the Turks was the priest Stipan Sorić from Bibinje. In 1468, the Venetian government fortifies Bibinje with a strong defensive wall and tower.