The oldest evidence of settlements on the island dates back to the Neolithic: fragments of pottery, weaving reels and a millstone have been recovered, as well as obsidian tools which show that Capraia was part of the route connecting Corsica and Sardinia with the continent. Subsequently Capraia is believed to have been the first Etruscan naval base and therefore certainly a Roman center of control of the maritime routes. In the late antiquity, starting from the 4th century AD, Capraia hosted an anchorite Christian community which chose to live in total isolation and, during the 5th century, saw the arrival of Zenobite monks who introduced the cultivation of the African vine and built the monastery of Santo Stefano.
Starting from the 9th century AD. Capraia was the scene of continuous clashes with pirates and was first abandoned for almost two centuries, then reoccupied alternately by Pisans and pirates until the battle of Meloria in 1284, which sanctioned its entry in the Genoese sphere of influence. Starting from 1540, the Genoese built the defensive system consisting of the fortress of San Giorgio and the three watchtowers. From 1873 to 1986 it was the site of a penal colony (Colonia Penale Agricola di Capraia).
Today the island of Capraia is a paradise of serenity and peace, in contact with nature and with a thousand-year history.