The armies of Napoleon crushed the Mamlukes at Imbaba and occupied Cairo. Napoleon's aim was to block British trade routes to India and to establish a Francophonic society in Egypt. He imposed a French administrative system and implemented public works projects to clean up and renovate the long-neglected country, clearing blocked canals, cleaning the streets and building bridges. Napoleon claimed to have respect for Islam and the Quran but the Egyptians did not believe him.

For all his attempts at "civilizing" the country, Napoleon failed to win the respect or allegiance of his subjects. His quixotic mission was doomed from the outset. Within a month of entering Egypt the British, under Admiral Nelson, attacked and destroyed the French fleet moored at Abu Qir Bay in Alexandria and the Ottoman sultan threatened war against the French.

Napoleon returned to France, leaving his armies behind. But his commander, General Kléber, was assassinated, leaving the army to General Menou, who claimed to have converted to Islam and declared Egypt a French protectorate. At this, the British occupied Alexandria and with the Ottomans captured Damietta and Cairo, forcing the French to surrender.

The Napoleonic invasion of Egypt had profound repercussions for the Arab and Muslim world which continue to influence the region's political and social development. This was the first European conquest of a major Arab country in the history of Islam and it signaled the rapid decline of Islam as a world political power. Although it could be said that the Ottoman Empire was by this time already a spent force, the humiliation of Napoleon's entry into Egypt was a devastating blow to pan-Islamic pride. It has been said that contemporary Muslim fundamentalism traces its psychological origins to this initial shattering defeat.