In 1580, sultan Murad III granted substantial privileges to the Cycladic islands, boosting trade and favoring local governments. Living conditions changed. Christians were free to build or repair their churches (Francois Richard reports 700 in total at that period, most of which were Orthodox). The faith of locals to Virgin Mary was very strong: they vowed to Her before each travel and they left their property to Her after their death.

According to Richard, residents ate barley bread and salted quail caught in their nets, drunk rain water from cisterns, cultivated vines, barley, beans, fava, millet, squash, cucumbers and melons. The wine was exported to Chios, Smyrni, Chandakas (Heraklion of Crete) and Constantinople. He also described the 1650 eruptions. In the end of 16th and 17th century the Kasteli of Pyrgos, the churches of the Transformation of Jesus, St. Theodosia, the church of the Virgin Mary, St. Catherine, Taxiarchis and many more, were built.

Franks had presence on the island even during the Ottoman Rule, while in 1642 Jesuit monks settled and got permission to build their first church. Since the Kasteli of Skaros was abandoned, they used building material from there.

In the late 17th century the privileged status of Santorini and other islands, together with changes in the community's organization, allowed financial growth- something more apparent in the 18th century. Merchants established close relations to famous ports in the Eastern Mediterranean and the Black Sea (Alexandria, Constantinople, Odessa), where they also founded important colonies.

Agricultural and marine activities continued to grow in Santorini; by the 18th century, the island had 9,000 people. In the 19th and the early 20th centuries, commercial sailing flourished and numerous ships from Santorini sailed the Aegean, transporting goods. On the eve of the 1821 revolution the Santorinian sail boats were several dozens, since the island had the third largest fleet in the Aegean Sea after the ones of Hydra and Psara. In 1856 it numbered 269 boats and the growth continued until the prevalence of steamboats in the late 19th century. Great example was Oia, the so called "village of the captains".

In the late 19th and early 20th centuries, industry also started developing in Santorini. The earthquake of 1956 accelerated the island's economic decline. The impressive recovery began in the 1970's, with the amazingly rapid growth of tourism.