[1][2] Cabrera is a UEFA Pro License coach with a wide range of experience in both professional and grassroots football projects.

[10] In 2016, he was appointed as the manager for Spanish club CF Rayo Majadahonda and spent a year coaching the team, before departing in 2017.

[13][14] On 8 January 2022, Bangladesh Football Federation (BFF) announced the appointment of Javier Fernández Cabrera as the new national team head coach.

Cabrera signed an 11 month contract during a meeting called by the BFF on 19 January 2022, where he was officially made the head coach of the Bangladesh national team.

[19] In June, Cabrera guided the team to three straight defeats, as Bangladesh finished bottom of their group in the 2023 AFC Asian Cup qualification – third round.