As we know was the Acropolis slowly turned back into a fortress under the Romans. However, this did not mean that it lost its religious function. The first major changes to the Acropolis came with the rise of christianity. Under Theodosius a process of christianization started and all heathen temples were burned down to the ground. Luckily enough even the christians saw the beauty of the Acropolis and they turned the most important buildings into churches.
The most important symbol of Greek heathenism, the Parthenon, was changed in the seventh century into a church for Aghia Sophia, the divine wisdom, and became later on the church of Panaghia Theotokos, the mother god. The temple of Nike and the Erechteum also became churches while chapels were built in the Propylaea and the temple of Asclepius. Later on the temple of Asclepius even became a monastery. Now Athens, which had become a small Byzantium provincial town after Justinianus, was again dominated by a major religious center, but this time a christian one. In 1019 emperor Basileios II went to the Acropolis to dedicate the trophies of his victory on the Bulgarians to the holy virgin, a new personification of Pallas Athena.
Othon de la Roche installed himself and his followers in the fortress Acropolis after the French crusaders had conquered Constantinopel. In 1209 he changed the Parthenon-cathedral with a Latin rite into the church of the holy Maria of Athens. On top of that they changed the look of the rock quite drastically: it got turned into a medieval fortress. A high tower was added to the Propylaea, the dukes of Athens installed themselves on the Acropolis. This was basically a setback to the times of king Cecrops.
In 1458 the Turks, under the leadership of Mehmed II the Conqueror, conquered the city which implied again big changes for the Acropolis. Again the Acropolis was used as a residence, but this time for the Turkish governor. The Parthenon became a mosque, and a minaret was added to it. Furthermore the Erechteum was changed into a harem and houses were built everywhere between the monumental Greek temples.
The Acropolis had suffered the most under the Turkish domination which lasted for almost four centuries. Until then only the inside was changed and damaged, but this no longer the matter when lightning struck into the Propylaea which were used by the Turks as a storageplace for gunpowder.