[3] From 2003 to 2005, Marcelino was in charge of the first team, finishing fifth and tenth in the second division, then signed with Recreativo de Huelva in the same league, which he led to promotion in his first season[8] and a comfortable mid-table position in the top tier in the following, which made him the recipient of his first Miguel Muñoz Trophy.

[9] Marcelino resigned at the end of the season and took over at former club Santander, leading the Cantabrians to a best-ever sixth-place finish, with the subsequent qualification for the UEFA Cup.

[13] On 13 December 2009, following a string of poor results (the last a 1–2 home defeat to Athletic Bilbao), Marcelino was fired by Zaragoza, with the Aragonese side nonetheless still above the relegation zone.

[17] Marcelino signed with Villarreal on 14 January 2013,[18] returning the team to the top flight at the end of the campaign[19] and going on to subsequently achieve three top-six finishes,[20] which included a fourth place and a semi-final run in the UEFA Europa League in 2015–16.

[21] On 10 August 2016, a few days before the first official match of the season, Marcelino was sacked for differences with the board of directors, particularly over the removal of Mateo Musacchio from club captaincy.

[35] Marcelino returned to Villarreal on 13 November 2023, signing a three-year contract;[36] he was their third manager of the campaign after Quique Setién and Pacheta, with Miguel Ángel Tena also having acted as interim for one game.