In Egypt, Morand fought under the command of Desaix. He was promoted to "chef de brigade" on the battlefield of the battle of the Pyramids on 21 July 1798. He remained with Desaix on the latter's expedition to Upper Egypt, and was placed in command of the garrison of Girgeh whilst Desaix headed further south. He repulsed a Mamluk attack on this town on 6 April 1799, and that August defeated Murad Bey at the battles of El Ganaim and Samannud. He was appointed "adjutant général chef de brigade" and governor of the province of Girgeh on 7 September 1799. Promoted to "Général de Brigade" on 6 September 1800, by May 1801 he joined Verdier's division to form the garrison of Cairo against the advancing Anglo-Turkish forces. A struggle for the city was avoided when, along with General Belliard, he signed a surrender agreement that would evacuate the remaining French troops. He himself left Egypt on 9 August 1801 and arrived in Marseille on 14 September. His letters and other writings during this period were later published.