He began his professional career with Valencia in 1984, going on to amass La Liga totals of 304 games and 16 goals over 12 seasons and also appearing for Real Madrid and Zaragoza in the competition, retiring in 1997.

His first senior post came in 2004, with Getafe, and he also managed Valencia, Atlético Madrid – where he won the 2010 Europa League – and Espanyol in the top division.

Abroad, he had spells at Benfica in the Primeira Liga and Watford (twice) in the Premier League, as well as stints in the United Arab Emirates and China.

[2] Flores moved to Real Madrid in summer 1994 on a four-year contract, and stayed with the capital side for two seasons, winning the league title in the first one[3] but being deemed surplus to requirements early into the 1996 preseason after complaining to newly-arrived manager Fabio Capello of toenail pains.

[23] At the end of the campaign, he led the team to the ninth position in the domestic competition, but also to two cup finals: the UEFA Europa League against Fulham (2–1 win)[24] and the Copa del Rey, lost to Sevilla.

[25] Frequently clashing with star player Diego Forlán during 2010–11,[26][27] Flores announced his departure from the Colchoneros before the season ended, with the team finally qualifying for the Europa League.

[33] His first match in charge took place two days later, and it ended with a 1–1 away draw against Almería in the domestic cup;[34] on 26 February, however, citing personal reasons, he resigned.

[35] On 5 June 2015, Flores was appointed the head coach of newly promoted Premier League side Watford, replacing Slaviša Jokanović and being the fifth man to hold that position in twelve months.

[49] His team were eliminated from the second round of the Spanish Cup on 16 December with a 5–0 loss at Atlético Baleares of the Primera Federación,[50] but seventeen days later achieved the first victory over Real Madrid in nearly nine years with a lone goal by Enes Ünal.

[53] On 18 December 2023, Flores was appointed at Sevilla, signing a contract until 2025;[54] he was their third coach of the campaign after José Luis Mendilibar and Diego Alonso.

[56] During a match at Getafe on 30 March 2024, Sánchez Flores, of Spanish Gypsy ancestry, was the victim of racist abuse from behind the coaches' benches.