[5] In the summer of 2006, immediately after retiring, Gómez started coaching, first with former club Albacete's youth team, with which he won the Copa del Rey of the category.

[7] Gómez re-joined former Real Madrid B coach Rafael Benítez in 2009, being named Liverpool's assistant while also training their reserve team.

[8] On 23 June 2010 he announced his move to Real Valladolid, signing for 2010–11 in division two after the dismissal of former Spain national team boss Javier Clemente.

[9] On 29 November 2010, following a 0–1 home loss against FC Cartagena, Gómez was fired by Valladolid, even though the Castile and León side ranked seventh in the league.

[10] From June 2011 to March 2013, he managed former club Albacete in the third tier,[11] and subsequently worked with Benítez at SSC Napoli,[12] Real Madrid,[13] Newcastle United,[14] Dalian Yifang FC,[15] Everton[16] and RC Celta de Vigo.