In 1975, Iseler was made an Officer of the Order of Canada "for his many services in the field of music in Canada, particularly for his development of the world-renowned Toronto Mendelssohn Choir". He was awarded the Order of Ontario in 1995. In 1997, he was named a Fellow of the Royal Conservatory of Music and an Adjunct Professor of Choral Music at the University of Toronto, where the Elmer Iseler singers became the official choir-in-residence. Following Iseler's death, the university created the Elmer Iseler Chair in Conducting.