by 2001, Humes had been named as the club's Academy director. He left his role in August 2001, when he re-joined Ipswich Town's Academy. He was promoted to the position of Academy manager in 2006 and remained in the role until 2009. Humes left his role in January 2009, before joining Colchester United as head of youth in June 2009. With Colchester, Humes helped to prepare Colchester's youth players for first-team action, with players such as Alex Gilbey, Sammie Szmodics, Tosin Olufemi and Freddie Ladapo all making their professional debuts in Joe Dunne's first-team squad under Humes' stewardship. During the 2013–14 season, Humes oversaw Colchester United's under-18 squad as they won the South East Youth Alliance league and the national Youth Alliance Cup. Following Colchester United's poor run of form in League One at the beginning of the 2014–15 season, it was announced on 1 September 2014 that Humes had replaced Joe Dunne as first-team manager after Dunne had left the club by mutual consent. His first game in charge was a 0–0 stalemate against Walsall at the Bescot Stadium on 6 September 2014, leading his side to their first clean sheet of the season. He oversaw his first victory of the season in only his second game in charge, a 2–0 away win against Leyton Orient on 13 September. Humes led the club to League One safety on the final day of the 2014–15 season. With Colchester needing results to go for them elsewhere, including either Crawley Town and Notts County to not win, or one of Crawley or Notts County to win and the other to lose alongside Crewe Alexandra, while beating promotion hopefuls Preston North End, who needed a win to guarantee promotion to the Championship. Colchester defeated their opponents 1–0 at the Colchester Community Stadium in a hard-fought match that meant they survived for another season by two points. Humes led Colchester to an unbeaten September 2015 following a winless start to the season. He guided his side to eighth position in League One by the end of September, which resulted in a nomination for League One Manager of the Month on 7 October. He faced competition from Bury's David Flitcroft, Burton Albion's Jimmy Floyd Hasselbaink and Southend United's Phil Brown. However, after seven defeats in the nine following games, including four back-to-back losses and a defeat to bottom club Crewe Alexandra on 24 November, Humes