当奥斯曼人到来的时候，希腊人兴起了两股移民运动。首先是希腊知识分子阶层向西欧的移民，由此激发了文艺复兴的到来。其次，一些希腊人离开了平原，躲进层峦的群山中。希腊是个多山的国度，而奥斯曼人从未成功地在山区建立他们的军事或者行政存在，因而在这种意义上来说，奥斯曼人从来没有完全征服希腊。在希腊大陆和岛屿上存在有许多秘密社群，如克里特岛上的Sphakiots、伊庇鲁斯的Souliots以及伯罗奔尼撒的Mani都是奥斯曼统治时期山区活跃的秘密社群。自16世纪末直至17世纪，许多希腊人开始从山区搬回平原地区。帝国推行的宗教自治社区“米利特”（Millet）制度将各个地区分划给宗教族群自治，这间接促进了东正教希腊人的民族凝聚力。希腊正教会作为民族-宗教社团，帮助全希腊各个地区（山区、平原、岛屿）的希腊人在艰难的奥斯曼统治下维系自己的种族、文化以及语言遗产。
奥斯曼统治下的希腊人不是承受异族统治的基督徒就是秘密基督徒（Crypto-Christians），他们表面上遵循伊斯兰教的教规，而秘密地实践希腊正教的信仰，以逃避苛重的捐税，而同时又不失去同希腊正教会的联系。然而那些真正皈依伊斯兰教的希腊人，即使他们保留了自己的文化和语言，也被同族的正教希腊人视为土耳其人。
Most of Greece was part of the Ottoman Empire from the 15th century until its declaration of independence in 1821, a historical period also known as Tourkokratia (Greek: Τουρκοκρατία, "Turkish rule").
The Byzantine Empire, which had ruled most of the Greek-speaking world for over 1100 years, had been fatally weakened since the sacking of Constantinople by the Crusaders in 1204.
Ottoman advance into Greece was preceded by victory over the Serbs to its north. First the Ottomans won at 1371 on the Maritsa River — where the Serb forces were led by the King Vukasin Mrnjavcevic, the father of Marko Kraljevic and the co-ruler of the last emperor from the Serbian Nemanjic dynasty. This was followed by another Ottoman victory in the 1389 Battle of Kosovo.
With no further threat by the Serbs, the Ottomans captured Constantinople in 1453 and advanced southwards into Greece, capturing Athens in 1458. The Greeks held out in the Peloponnese until 1460, and the Venetians and Genoese clung to some of the islands, but by 1500 most of the plains and islands of Greece were in Ottoman hands. The mountains of Greece were largely untouched, and were a refuge for Greeks to flee foreign rule.
Cyprus fell in 1571, and the Venetians retained Crete until 1670. The Ionian Islands were only briefly ruled by the Ottomans (Kefalonia from 1479 to 1481 and from 1485 to 1500), and remained primarily under the rule of Venice.