In the summer of 2005, Faber became coach of PSV's reserve team Jong PSV. In the 2005–06 season of the Beloften Eredivisie, Faber's team narrowly escaped relegation. But in September 2006, Faber left Jong PSV. He claimed that the team was neglected by PSV and not strengthened as promised. Faber's desire was to remain at the club, but the board did not offer him another position. Faber proceeded to join FC Eindhoven as their assistant manager in December 2006. In October 2007, FC Eindhoven sacked their manager Louis Coolen. Faber stepped up as caretaker manager for two months. He went back to his position as assistant when Gerald Vanenburg was appointed as the new manager in December. Seeking a new challenge, Faber announced in February 2008 he would leave FC Eindhoven at the end of the season. Before his departure, Faber had to become FC Eindhoven's caretaker manager again after Vanenburg resigned in April. He coached the team in the remaining three matches.