The article discusses the French policy regarding the Christian minorities of Ottoman Egypt and Ottoman Syria during Bonaparte’s Eastern expedition in 1798–1801. A special attention is paid to plans of the French military command aimed at involvement of Egyptian Copts and Syrian Christians in cooperation with the French as civil officials in the occupation administration and as auxiliary military forces. The article also analyzes propagandist proclamations of the French and their practical actions towards local Christians in Egypt and Syria, as well as the reaction to them from Christian minorities, Muslim majority and Ottoman authorities. Particular attention is paid to the analysis of contradictions and duality of the policy pursued by Bonaparte and his successors, commanders-in-chief of the French army in Egypt – Generals Kléber and Menou, which, on the one hand, wanted the Eastern Christian communities to be allies of France, and on the other, did not dare to openly express sympathy for Christians in order not to irritate Muslims and not to give the warfare the nature of a religious war. The article concludes that this inconsistency was actually one of the reasons for the failure of the French expedition, making it impossible to increase and strengthen the French troops which turned out to be cut off from communications with France.