The monastery of St. Francis of the Franciscans was founded in the area today covered by the building that hosts the Archaeological Museum of the city, i.e. by the eastern curtain wall of the old enceinte. The exact date of its foundation is not clear but it already existed by 1242. Of the huge church, with the voluminous polygonal apse, which projected proudly over the eastern city walls, a small section has been recently revealed. The building, which was turned into a mosque, dedicated to the Sultan Mehmet IV (Hünkar Çamii, i.e. imperial mosque), was ruined by the earthquake of 1856, except for a chapel which continued to be used as a mosque and was later turned into a warehouse for antiquities. Debris from the demolishment of the church was used for the construction of the Yeni Vizier Çamii (St. Titus) and other public buildings. The elaborate door-frame of the northern entrance of the large building that hosted the Ottoman Military Quarters was therefore identified as the door-frame that was donated to the monastery of St. Francis by the Pope Alexander V (1409-141), who lived as a monk in the Franciscan monastery of St. Antony in Kares, near Neapolis, in the county of Mirabello, under the name Petros Philarges. Nevertheless, only the pair of rounded column pedestals, made of marble in the color of porphyry and decorated with elaborated acanthus-leaves, perhaps even the pair of pilaster-capitals made of greyish marble, could originate from the Venetian church, probably from different door-frames. The rest of the door-frame of the Ottoman building, including the door-lintel with the oriental relief with the acanthus leave, is in its first use.

Ruins of the Venetian church were still visible until the beginning of the 20^th c. Between 1904 and 1907 the first small-scale building of the Archaeological Museum was constructed on the site. In 1937 the still standing chapel was also demolished for the construction of the modern building of the Museum. Recently, excavations that were conducted during the construction of an additional compartment of the Museum brought to light the underground floor of the polygonal apse and the southern wing of the transept, which was functioning as a burial crypt, It was also documented that the rest of the building’s remains extend further to the West, underneath the foundation of the modern construction.