[10] On 12 June 2013, Cardoso was presented at FC Shakhtar Donetsk, being appointed manager of the under-21 squad while also working as a coordinator for the club's youth setup.
[12] On 12 June 2017, Cardoso was appointed at the helm of Primeira Liga club Rio Ave F.C., replacing departing Luís Castro.
[17] On 12 November 2018, Cardoso took over La Liga side RC Celta de Vigo, in the place of sacked Antonio Mohamed.
[20] On 28 May 2019, Cardoso was appointed as head coach of Greek Super League side AEK Athens F.C., replacing Manolo Jiménez on a two-year deal.
[25] On 12 January 2024, Cardoso was appointed as head coach of Tunisian Ligue Professionnelle 1 side Espérance Sportive de Tunis, replacing Tarek Thabet.
[26] After being sacked by Espérance in October 2024 following a poor start to the season, South African Premiership club Mamelodi Sundowns appointed Cardoso in December 2024.