Despite its losses during the Ottoman era, the Monastery continued to retain ownership of its Byzantine dependencies. In fact, new estates that the Monastery had not had in the Byzantine period now appeared among its possessions: Chalkidiki (Ierissos, Kassandra, Ormylia, Sidirokaussia), Strymon (present day Nea Kerdylia, etc.), the islands Thassos, and Agios Efstratios in the North Aegean, and other dependencies in Crete, Asia Minor and Bessarabia. According to C. Pavlikianof, in 1535, Suleiman the Magnificent issued a firman (i.e., an official Ottoman decree) that authorized the voevoda (prince) of Moldavia and Wallachia to restore the Monastery's buildings without expanding them. Perhaps this edict refers to the maritime tower and the barbican (i.e. defensive fortification), which according to an inscription was completed when Germanos was Abbot, with the sponsorship of the Prince John Peter (perhaps Peter IV Rares of Moldova) and a monk named Joasaf.
According to Smyrnakis, in 1548, an Ottoman officer named Ibrahim ordered two Muslims, Mustafa and Ali, to visit Karakallos Monastery to measure the cathedral before its restoration was allowed, as was finally the case.
In 1708, Komnenos writes that in the 16th century, the Monastery was renovated at the expense of two generous sponsors: The Prince Neagoe Bassarab of Wallachia, and a prince named Peter. In fact, according to P. Androudis, the impressive tower has typical features of the 16th century, indicating it might have been one of the structures included in the above-mentioned work.
In the 17th century, Artchil, the King of Iberia, together with his brother George Vachtags (1674) and the monk Joashaff in the 18th century, played an active role in the Monastery, which grew considerably during that time: According to some testimonies, the population of monks practising in the Monastery and its dependencies reached several hundred.
