On 9 February 1794, Merlin took a staff position with the Army of the Eastern Pyrenees and fought in the War of the Pyrenees against the Kingdom of Spain. During the conflict he was wounded in the left leg by a bursting howitzer shell. He was assigned to the 4th Hussar Regiment as adjutant general "chef de brigade" on 13 June 1795. He served with the regiment in the Army of Sambre-et-Meuse. During the Rhine Campaign of 1795 on 1 October, the 4th Hussars were part of Paul Grenier's division. Merlin was wounded in the right arm by a saber stroke at Steinbach on 15 October 1795 in a minor French victory during the retreat.