In 2001, Flores began his managerial career when he took charge of Real Madrid's youth team. His first senior post came in 2004, with Getafe. He returned to Valencia in 2005, being dismissed after two years and going on to work with Benfica, Atlético Madrid – where he won the 2010 Europa League – Al-Ahli, Al-Ain and Watford, before being appointed at Espanyol in 2016.