In 1479, Leonardo III Tocco (1449-1479) withheld tribute payments to the Ottoman Empire, resulting in a temporary Ottoman occupation of the castle. It wasn’t until 1502 that the Venetians briefly regained control of the castle. During the Ottoman presence at the castle (1479-1502), minimal efforts seem to have been made to modernize its fortifications. On August 23, 1502, Venetian Admiral Pesaro, commanding a fleet transporting Venetian, French, and Papal forces, arrived in Lefkada with orders to capture the castle of Agia Mavra. Following a seven-day siege, he successfully overcame the resistance of the Ottoman soldiers guarding it, raising the flag of the Venetian Republic over the castle for the first time.
The following year, in 1503, the Venetians initiated reinforcement works on the fortress. This coincided chronologically with the gradual adoption of gunpowder and the extensive use of firearms in Europe, necessitating the adaptation of fortifications to the new defensive requirements. Specifically, the most significant tasks carried out during this brief period included the construction of a new bastion with a casemate (casamatta) in the southwest (SW) and the foundation of another bastion to the north (known as the Pantokrator bastion).