As a manager, he won two Uruguayan championships with Nacional and La Liga titles with both FC Barcelona and Real Madrid.

Fernández and Balmanya made their La Liga debuts for Barça together on 10 November 1935 in a 1–0 defeat to RCD Español.

After retiring as a player due to a serious knee injury, Fernández began coaching and in 1946 he guided Nacional to a Uruguayan championship.

With a squad including Velasco, Ramallets and Estanislao Basora, he helped the club win two La Liga titles in 1948 and 1949.

He was appointed coach at Real Madrid for the 1953–54 season and with a team that included Alfredo Di Stéfano, Francisco Gento, Miguel Muñoz, Luis Molowny and Héctor Rial he guided the club to their first La Liga title since 1933.