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In the intervening years the monastery declined until Prince Ioannis Ugljesa, impressed with the reputation of the Blessed Simon, petitioned Cyril Lucaris, Patriarch of Constantinople, to reactivate the empty monastery. With this permission, Ugljesa immediately built an entire monastery, but, after a brief period of prosperity, Athos and the monastery entered into the chaos and ruin of the ascendency of the Ottoman Turks over the area. Most records of this period were destroyed in a great fire of 1580. Yet, the monastery had functioned without interruption. On [[December 11]], 1580, the monastery suffered total destruction by fire killing many of the monks. The survivors, however, were able to save the coffers of the monastery, which apparently were considerable as the Simonopetra monks were able to buy the assets and administration of a neighboring monastery, [[Xenophontos Monastery (Athos)|Xenophontos Monastery]] as a temporary home. As rebuilding the monastery required consideration funds, the [[abbot]], Evyenios, journeyed to Wallachia in 1587 to raise money. Earlier in 1566, the Great Postelnik Gheorma in Wallachia had donated the Monastery of St Nicholas in the suburbs of Bucharest to Simonopetra monastery as a metochi. In the meantime the rebuilding of the monastery at Mt. Athos continued so that by 1586 the monks were back in their own monastery.
On [[June 8]], 1622, Simonopetra experienced a second fire. However, this one only caused minor damage, and by 1623, the abbot, Timotheos, dedicated the
restore ''katholikon''. After this time the monastery appeared to enter a period of decline. By 1745 the population of the monastery had decreased to five. Finally, in 1762, the monastery was closed and taken over by the central administration of Athos (the Great Mese) to satisfy its creditors. In the meantime, Fr. Ioasaph of Mytilene managed to raise enough funds to buy back the monastery's metochia and restore parts of the monastery. However, the revival was accompanied by apparent financial wrongdoings that brought Patriarch Kallinikos into assert control and eventually assign a new abbot, Dionysios.
This period of chaos continued when the effects of the Greek independence movement caused the occupation of Mt. Athos by the Turks. While the monastery continued to function, the high taxation by the Turks and looting resulted in the departure of all the monks by 1823. After the Turks departed in 1830, the monastery returned to a life of constant turmoil. This turmoil continued until the destructive fire of [[May 27]], 1891. Through the efforts of the abbot, Neophytos, and both with the cooperation and demands of the Russian Church Simonopetra was again restored and was flourishing by the turn of the century.