When Austria succeeded in suppressing the rebellion, Van Merlen was one of those who fled to France, settling in Douai in December 1790. On 15 July 1792, he was appointed 2nd Lieutenant in the Belgian Legion, part of the Army of the North under Charles François Dumouriez. He fought at Jemappes and Neerwinden, becoming a 1st Lieutenant on 13 March 1793 and Captain on 11 August the same year. At the battle of Lincelles, two of his ribs were crushed by a rifle bullet. The following year, he became adjutant to Jean-Baptiste Dumonceau, and took part in the battle of Tourcoing.