Born in Barcelona, Spain, Clotet only appeared for local amateurs CF Igualada as a player. He became a coach while still in his 20s, starting with UE Cornellà then moving to RCD Espanyol's youth teams. Clotet began the 2006–07 season with another side in his native region, UE Figueres, being fired after only nine matches as they eventually suffered relegation from Segunda División B. He subsequently returned to his previous club, still in charge of the youths. Clotet returned to senior football in the 2009–10 Segunda División B campaign with Espanyol's reserves. He met the same fate as in his previous experience: he was sacked following the seventh round and the team were relegated.
On 11 July 2012, Clotet was appointed as manager of Tercera División club Atlético MalagueñoMálaga CF's reserveswhere he helped develop several players who would reach the first team shortly after; their progress was aided by Málaga's unstable economic situation. He left the club after only one season, not being able to attain promotion.
On 19 November 2013, Clotet was appointed academy consultant at Swansea City as part of Michael Laudrup's coaching staff. In May of the following year, he was promoted to assistant manager under Garry Monk. In November 2015, Clotet was offered the manager's job at Championship club Brentford, but rejected the offer out of loyalty to Monk. He left his post at the Welsh club on 9 December of that year alongside first-team coaches James Beattie and Kristian O'Leary, following the sacking of Monk.
Clotet was appointed manager of League One club Oxford United on 1 July 2017. He was sacked on 22 January 2018, with a record of 12 wins from 36 matches in charge.
Birmingham City
When Monk took over as manager of Championship club Birmingham City on 4 March 2018, Clotet was appointed as his assistant. He became caretaker head coach in June 2019 after Monk was sacked; ahead of the November meeting between Birmingham and Monk's new club, Sheffield Wednesday, Monk claimed he had made an "error of judgment" in working with Clotet, suggested he was untrustworthy, and refused to shake his hand. After six months, during which Clotet made a start on implementing the board's footballing philosophy as well as demonstrating "coaching expertise, man-management and leadership skills, allied to exemplary professional conduct", and integrated the 16-year-old Jude Bellingham into a regular role in the first team, he was appointed as head coach on a permanent basis. Two months with only one league win at the end of the year was followed by the arrival of striker Scott Hogan, whose return to form sparked a ten-match unbeaten run in early 2020 which left the team 16th in the table when football was suspended due to the COVID-19 pandemic. On 8 June, Clotet confirmed that he would leave the club at the end of the season to "explore other coaching opportunities", but after a series of poor results, he left by mutual consent on 8 July with four matches of the season remaining.
Media
Clotet worked as a pundit on Sky Sports' La Liga review, and also wrote a column for daily newspaperMarca.