Gombau moved to Hong Kong to join Kitchee as the club's head coach in 2009. Under Gombau, Kitchee won two league titles, two FA Cups and one League Cup. Before the 2012 AFC Cupaway match to Tampines Rovers, Kitchee captain Chu Siu Kei applauded the contribution of Gombau to the team, saying: "The coach understands that the players might be smaller than those in the other teams, but using the ball more on the ground gives us an advantage over our opponents. We have more control of the game now".
On 30 April 2013, it was announced that Gombau would leave Kitchee to coach Adelaide United in the A-League. He signed a two-season deal, arriving at the club in July 2013. His first two signings were compatriots and Barcelona youth products Sergio Cirio and Isaías Sánchez. Gombau also brought his long-time assistant coach Pau Marti to work alongside existing assistant coach Michael Valkanis. Gombau stated that he wants to implement a possession-based football style at Adelaide. Gombau actively exercised his ambition to develop South Australian grassroots football by hosting free seminars for local coaches. Gombau's United won the inaugural FFA Cup by defeating Perth Glory 1–0. Gombau left the club in July 2015 to take up a youth coaching role in the United States.
Known as a developer of talent, on 28 June 2016, Gombau was appointed as head coach of Australia U-23 in place of Aurelio Vidmar, under whom the team failed to qualify for the Olympics.
On 1 November 2017, Gombau was assigned as head coach of Western Sydney Wanderers following the departure of Tony Popovicat the beginning of the season and Hayden Foxe acting as interim coach in the first four rounds. After just six months in charge, 19 April 2018, the club announced they had terminated Gombau's contract after failing to qualify for the 17-18 A-League Finals Series.
On 1 August 2018, Gombau was appointed as head coach of Delhi Dynamos following the departure of Miguel Ángel Portugal, under whom the team failed to qualify for the ISL Playoffs. Under Gombau team is not qualified for playoffs and placed eighth in the points table but the performance of the team improved and Gombau extended his contract and the club changed its base from Delhi to Odisha and Kalinga Stadium as home ground because of the high operational cost and low attendance in the stadium and he stayed with the rebranded team.
Odisha FC
Gombau was extended his contract to the rebranded club Odisha FC and they brought some players and extended some old players and they became finished sixth in the table and not qualified for the playoffs. The club and Josep Gombau have amicably parted ways due to the coach's familial obligations. Club President Mr. Rohan Sharma said, "Some things in life are more important than football. I'd like to thank Coach Gombau and his coaching staff from the bottom of my heart for all that they have done for the club. The whole coaching staff was such a positive influence for the club. No matter where they all go in life they will always have a home in Odisha! Josep expressed, "It wasn't an easy decision to make. I have enjoyed my time at Odisha and I am proud of what I built there. It is with some regret that I can't finish what I started, but I will always be rooting for the success of Odisha FC." Josep had joined Odisha FC ahead of the fifth season in 2018. He continued for the second consecutive season in 2019-20 and took OFC close to the playoffs spot.
Queensboro FC
In July 2020, Gombau was announced as the first-ever head coach and sporting director for David Villa's USL Championship club Queensboro FC.
Personal life
Gombau is married, his wife name is Romania Gombau and has two daughters: Bruna and Maria.
