Flemming Windekilde has conducted several Danish choirs, ensembles, and orchestras, including the Danish National Vocal Ensemble, Athelas Sinfonietta Copenhagen, Aalborg Symphony Orchestra and the vocal ensembles Vor Frue Kantori and Ars Nova Copenhagen. In 2001, Flemming Windekilde was appointed the choral leader of the youth choirs of Sankt Annæ Gymnasium.
Flemming Windekilde has conducted the Copenhagen based chamber choir Hymnia since its formation in 1983. Hymnia is one of Denmark’s leading choirs, specializing in new and complex choral music and late Romantic works. Together with Hymnia, Flemming Windekilde has recorded 15 CDs, won first prizes at several international choral festivals. They were named “Artists of the Year” in Copenhagen in 1996. Since 2001, Flemming Windekilde has regularly conducted the various choirs of DR (Danish Broadcasting Corporation).