During the years of Ottoman control from 1517 on, custody of the Basilica was bitterly disputed between the Catholic and Greek Orthodox churches.

From 1831 to 1841 Palestine was under the rule of Muhammad Ali of Egypt. During this period the town suffered an earthquake as well as the destruction of the Muslim quarter by troops, apparently as a reprisal for a murder. In 1841, Bethlehem came under Ottoman rule once more, and so it remained until the end of the First World War and the imposition of the British Mandate of Palestine.