In Paris, Zajączek quickly became involved with the active emigre groups there. Hoping to sway revolutionary France into supporting the Polish cause, many Poles, including him, volunteered to join the French Revolutionary Army, eventually leading to the creation of the Polish Legions in Italy led by Jan Henryk Dąbrowski, which became a part of Napoleon's army. On 8 March 1797 Napoleon ordered that Zajączek should be recognized as an active brigade general of the French army. That year he published a brochure on his experiences of the 1794 war, "Histoire de la révolution de Pologne en 1794", in which he tried to justify his actions. Zajączek was, however, still unpopular among the Polish troops, many of whom blamed him for the fall of Praga; due to frequent personal conflicts, Zajączek chose to remain with the French army, rather than joining the Legions themselves. Over the coming years, he took part in the French Revolutionary Wars. He took part in the 1798 Egyptian Expedition. There he also served as a governor of several provinces, first, from July that year, of the Monufia Governorate, later, from January 1799, simultaneously of the Faiyum Governorate and Beni Suef Governorate. On 25 January 1800 he defeated Murad Bey at the Battle of Sédiman. In 1801 he was promoted to division general, and later took part in the failed defense of Alexandria.