In his coaching career, Nunes worked with several Colombian teams such as Deportivo Cali, América de Cali and Millonarios. He was the assistant coach of José Hernández, who was in charge of the Panama national football team during the 2006 World Cup qualification. He also coached Universitario de Deportes in the season 2006/2007 terminating his contract by mutual agreement with the chairmen on 15 February 2007.