當奧斯曼人到來的時候，希臘人興起了兩股移民運動。首先是希臘知識分子階層嚮西歐的移民，由此激發了文藝復興的到來。其次，一些希臘人離開了平原，躲進層巒的群山中。希臘是個多山的國度，而奧斯曼人從未成功地在山區建立他們的軍事或者行政存在，因而在這種意義上來說，奧斯曼人從來沒有完全徵服希臘。在希臘大陸和島嶼上存在有許多秘密社群，如剋裏特島上的Sphakiots、伊庇魯斯的Souliots以及伯羅奔尼撒的Mani都是奧斯曼統治時期山區活躍的秘密社群。自16世紀末直至17世紀，許多希臘人開始從山區搬回平原地區。帝國推行的宗教自治社區“米利特”（Millet）制度將各個地區分劃給宗教族群自治，這間接促進了東正教希臘人的民族凝聚力。希臘正教會作為民族-宗教社團，幫助全希臘各個地區（山區、平原、島嶼）的希臘人在艱難的奧斯曼統治下維係自己的種族、文化以及語言遺産。
奧斯曼統治下的希臘人不是承受異族統治的基督徒就是秘密基督徒（Crypto-Christians），他們表面上遵循伊斯蘭教的教規，而秘密地實踐希臘正教的信仰，以逃避苛重的捐稅，而同時又不失去同希臘正教會的聯繫。然而那些真正皈依伊斯蘭教的希臘人，即使他們保留了自己的文化和語言，也被同族的正教希臘人視為土耳其人。
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.