He pursued further studies in Dresden and Leipzig during the summers of 1871 and 1872 with Benjamin Robert Papperitz (organ) and Louis Plaidy (piano).

He once again replaced his brother in 1876, taking over the role of organist at the Notre-Dame Basilica-Cathedral in Quebec City where he remained through 1915.

From 1877 to 1917 Gagnon taught at both the École normale Laval and the Petit Séminaire de Québec in addition to maintaining a private studio.

He became the first director of the music conservatory at Université Laval in 1922, and taught at that school until his death in Quebec City in 1930.

His pupils included Joseph-Arthur Bernier, Joseph-Daniel Dussault, Léo-Pol Morin, and his son Henri.