The notion of annexing Egypt as a French colony had been under discussion since François Baron de Tott undertook a secret mission to the Levant in 1777 to determine its feasibility. Baron de Tott's report was favorable, but no immediate action was taken. Nevertheless, Egypt became a topic of debate between Talleyrand and Napoleon, which continued in their correspondence during Napoleon's Italian campaign. In early 1798, Bonaparte proposed a military expedition to seize Egypt. In a letter to the Directory, he suggested this would protect French trade interests, attack British commerce, and undermine Britain's access to India and the East Indies, since Egypt was well-placed on the trade routes to these places. Bonaparte wished to establish a French presence in the Middle East, with the ultimate dream of linking with France's ally Tipu Sultan, ruler of Mysore in India.

As France was not ready for a head-on attack on Great Britain itself, the Directory decided to intervene indirectly and create a "double port" connecting the Red Sea to the Mediterranean Sea, prefiguring the Suez Canal. At the time, Egypt had been an Ottoman province since 1517, but was now out of direct Ottoman control, and was in disorder, with dissension among the ruling Mamluk elite. According to a 13 February report by Talleyrand, "Having occupied and fortified Egypt, we shall send a force of 15,000 men from Suez to the Sultanate of Mysore, to join the forces of Tipu Sultan and drive away the English." The Directory agreed to the plan in March, though troubled by its scope and cost. They saw that it would remove the popular and over-ambitious Napoleon from the centre of power, though this motive long remained secret.