Following retirement from playing, Chu took over the managerial position at Fukien in 2001. Despite working with a limited budget, Fukien were able to stave off relegation from First Division during Chu's first three years at the club while occasionally scoring upset victories over table toppers Happy Valley and Sun Hei. During his tenure, he discovered and signed talent players such as Tong Kin Man, Zhang Chunhui and Wong Chin Hung. After a disappointing 8th place finish during the 2004-05 season, Fukien were not originally relegated from the First Division. However, the club chose to voluntarily relegate themselves to the Second Division and Chu left the club. In 2006, Chu joined Kitchee as a coach. Players such as Ngan Lok Fung, Li Ngai Hoi, Tsang Kin Fong trained under his tutelage at Kitchee's academy and later became professional footballers. After the departure of Dejan Antonić on 27 December 2007, Chu was asked to become the caretaker. His managerial debut for Kitchee came on 11 January 2008 which resulted in a 1-1 draw against Eastern. On 14 November 2013, manager Àlex Gómez suddenly resigned his position. Chu and Cheng Siu Chung were named co-caretakers of the club until the end of the 2013-14 season. Both Chu and Cheng were responsible for leading Kitchee to an undefeated season and the league title. On 5 March 2016, history was repeated as :es:Abraham García Aliaga|Abraham García suddenly resigned as manager of Kitchee. Chu was named caretaker for the remainder of the season. Ahead of the 2016-17 season, Chu was named the permanent manager as well as Director of Football for the club. Kitchee were rewarded for their decision as Chu managed the first team to a domestic treble, capturing the Premier League, the Hong Kong FA Cup and the Senior Shield. The only blemish on their historic season was a 2017 AFC Champions League qualifying playoff round loss to Ulsan Hyundai. Kitchee had taken the Korean club to penalties but came up just short of qualifying for the Champions League group stage for the first time. For his achievements, Chu won the Hong Kong Coach of the Year award for 2017. On 3 July 2019, Chu stepped down from his head coaching duties at Kitchee. On 11 August 2019, Chu was appointed as an assistant to Hong Kong head coach Mixu Paatelainen until the end of the year. On 23 March 2020, Chu was named as caretaker of Kitchee until the end of the 2019–20 season following Blaž Slišković's decision to step down as head coach.
