Troglio then went on to coach Godoy Cruz de Mendoza in Primera B Nacional but he left in the middle of the tournament to take on in March 2005 a demoralized Gimnasia and helped keep the team in the Primera. The next season he led them to 2nd place in the Apertura tournament, equalling their highest finish ever.
After the successful 2005 campaign, Gimnasia has performance declined markedly. Following a series of defeats in national and international competitions, including a 7:0 derby defeat to Estudiantes de La Plata, Troglio resigned on April 2007, and was temporarily replaced with former aide Ricardo Kuzemka. Nevertheless, Troglio's status with fans did not deteriorate strongly, with most press articles blaming club president Juan José Muñoz on the poor performances of the team.
In 2007, after Jorge Burruchaga's departure of Independiente, Troglio was hired to manage this institution. In March 2008, after an erratic season start, Troglio was sacked and replaced by Miguel Angel Santoro.