By the time of his retirement in 1898, he was a Chevalier of the Légion d'Honneur and had built, restored, or repaired over 400 organs, primarily in the churches of Belgium and France.

Three years later, he reorganized the company as the Société Anonyme pour la Fabrication des Orgues, Établissement Merklin-Schütze.

[1] In 1867 the company's grand organ built for the Basilica of St. Epvre in Nancy received a Gold Medal at the Exposition Universelle in Paris and Merklin was made a Chevalier of the Légion d'Honneur.

In 1879, he gave half the shares in the Lyon company to Charles Michel, who had married Merklin's daughter Marie-Alexandrine in 1875.

He went to Madrid at the outbreak of World War I to establish a firm there and wrote a treatise on the history and construction of Spanish organs published in 1924.