After retiring as a player, Garnero became the assistant manager to Jorge Burruchaga at Arsenal de Sarandí. He has also held coaching positions at Estudiantes de La Plata and Independiente. In July 2008 he was appointed as manager of Arsenal de Sarandí as replacement for Gustavo Alfaro. On 25 April 2009 he was sacked as manager of Arsenal de Sarandi. On 20 May 2010 was named as Independiente's new coach, the former Diablos Rojos player replaces Americo Gallego, who left the club a few days ago. On 21 September 2010 Independiente have parted ways with coach Daniel Garnero by mutual consent, just four months after he took over from Americo Gallego at the Argentine giants.