Van Merlen was promoted to Major on 6 April 1807, and to Colonel on 5 March 1808. He was placed in command of the newly formed "Gardes te Paard" (Horse Guards) Regiment, which consisted of hussars and cuirassiers. However, he seems to have offended King Louis and had to leave the court, becoming colonel of the 3rd Hussars who were already serving in the Dutch Brigade and fighting in the Peninsular War. He joined his new regiment in Spain and led it in the battles of Talavera, Arzobispo, Almonacid and Ocaña. By this time casualties had reached such a level that Colonel van Merlen sent two squadrons of sick and disabled back to Holland in June 1810, retaining just a single squadron under his command in Spain.