[9] On 4 November he returned to Prat for a third stint,[10] but was relieved from his duties at the end of the season after failing to achieve promotion.
[11] He was dismissed on 26 October,[12] and only returned to coaching duties the following 16 June, after being named UD Las Palmas Atlético manager.
[13] Márquez achieved promotion to the third tier as champions with the B-team, and on 3 July 2017 he was appointed manager of the main squad in La Liga, after agreeing to a one-year contract.
[15] On 26 September 2017, after just six league matches in charge, Márquez resigned as manager after overseeing a 0–2 home defeat against CD Leganés just two days earlier.
[23] The announcement came after he had led the team in the 2020–21 season to a 5th-place finish on the league table, failing to qualify for the playoff by two points.
[27] On 20 July 2024, Márquez was appointed as the head coach of Indian Football Team succeeding the post of Igor Stimac who was replaced by the AIFF.
Both were also at FC Goa, and similar to Marquez, would do both jobs until the end of the season, before solely working for the national team.