Theo Bos served as manager of FC Den Bosch from 2005 to 2009. Later in 2009, it was confirmed he would make a comeback at Vitesse, this time as a head coach. He was removed from his managerial duties in October 2010 by new club owner, Georgian businessman Merab Jordania.
He served as head coach of Dutch Eerste Divisie club FC Dordrecht in the 2011–12 season, replacing Henny Lee who opted to leave the club in order to join FC Utrecht in the Eredivisie league. In January 2012 he was forced to take indefinite leave of absence after he was diagnosed with pancreatic cancer; his place as head coach was temporarily taken by assistant Virgil Breetveld on an interim basis. After the end of the season it seemed like Bos would return to being in charge of the team; however, on 14 July 2012, it was announced that he had been forced to take indefinite sick leave due to his health conditions.