As well as working as assistant at several clubs, he managed Cornellà, Figueres, Espanyol B, Halmstad, Atlético Malagueño, Oxford United, Birmingham City, SPAL and Brescia.

[4] Clotet began the 2006–07 season with another side in his native region, Figueres, being fired after only nine matches as they eventually suffered relegation from Segunda División B.

On 20 September 2011, Clotet joined Viking as coach in new manager Åge Hareide's backroom staff for the 2012 Norwegian Premier League season.

[13][14] 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.

[18][19] A month later, after the appointment as manager of Thomas Christiansen, who was intending to bring in his own backroom staff, director of football Victor Orta confirmed that Clotet wanted to leave to seek a new challenge.

[26] 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[27][28] which left the team 16th in the table when football was suspended due to the COVID-19 pandemic.

[35] On 16 January 2023, however, Clotet was reinstated as head coach with immediate effect,[36] only to be dismissed once again less than a month later, on 6 February, after he failed to improve the team results.

[40] The start of the second-tier 2023–24 Russian First League campaign was below expectations as well, with five wins and five losses in the first 12 games, and in October 2023, Torpedo announced the dismissal of Josep Clotet.

[44] Clotet worked as a pundit on Sky Sports' La Liga review, and also wrote a column for daily newspaper Marca.