Girona were relegated from LaLiga after their 1-1 draw against Elche at Estadi Montilivi, sealing a 19th-place finish and an exit from the Spanish top tier after a four-year stay.
"Having taken charge in the summer of 2021, Míchel has been a key figure in the sporting growth and consolidation of Girona FC's playing style," the club said in a statement on their website.
Girona fans criticised Míchel, whose side failed to win any of their last eight league games, for being distracted by a potential move to Ajax amid a heated relegation battle.
"Over his seasons at the helm of the first team, he has managed a total of 221 official matches, becoming one of the most important coaches in the Club's recent history. In his first season, he led the team to a memorable promotion to LaLiga through the play-offs, culminating in Tenerife on a night that has become historic for Girona fans," the statement continued.
Míchel joined the Catalan club in 2021 and immediately won promotion to LaLiga in his first season in charge. In the club's second season in LaLiga, Míchel and Girona qualified for the UEFA Champions League for the first time in their history. Míchel was named LaLiga Manager of the Season following this historic success with the Blanquivermells.
Míchel leaves the club as the manager with the second-most matches led in its history (221) and second-most wins (91).
The 50-year-old Madrid-born manager previously worked for Rayo Vallecano and Huesca after a 20-year playing career.
Close to agreement with Ajax
The news of Míchel's departure from Girona follows a day after it was reported that the manager was closing in on a full agreement with Eredivisie giants Ajax.
According to ESPN, Ajax and Míchel are negotiating the fine details, primarily the length of the Spaniard's contract and the composition of his staff. Both parties are intent on reaching a full agreement soon.
The 50-year-old manager was also linked with a move to Bayer Leverkusen, who reportedly turned down the deal due to Míchel's "poor grasp of the English language."
An announcement from Ajax is soon expected.