May 2008, Flores took over Benfica. Where he achieved good results, a third league win of the season and first in team history League Cup. But he made only temporarily stay in Benfica, Benfica end of the season he and friendship broke up.
October 2009, Flores came to the bigger platform - Atletico Madrid, Atletico Madrid offered him a one-year contract. Atletico this season, suffered the worst start since 2000, former coach in the Champions League after a 0-4 defeat to Chelsea after class. Atletico, Flores successfully activated state Fran poor season start, he and Reyes, Aguero jointly form a powerful attack. Although Atletico got only ninth in the league final, but scored the King's Cup and the European League final, in the European Union they beat Fulham 2-1 to win the King's Cup it lost to Sevilla. Flores of the European Cup is Atletico since 1961-62 Super Cup first European trophy, the Champions League and subsequently beat Inter Milan in the European Super Cup.
2010-11 season, Atletico performance is still not satisfactory. Fran increases with age, state and downs, his attitude was often rejected Flores. So Flores decisively stripped of his starting to rookie Diego Costa replaced, resulting in discord with Fran, but was still the Brazilian Diego Costa also replace Fran's first staged hat trick. This season Aguero is in his hands to become top scorer, currently Manchester United goalkeeper De Gea Flores men are one step from the third goalkeeper on the main lift. End of the season only to get the league Atletico seventh, while access to the European Cup qualification, but Flores at the end of the season still left Atletico.
Flores Since then flee to Europe, although there have been rumors and Spartak Moscow, he chose Qatar giants Ahly, once in office he won the League Cup for the team, once President Cup, but did not get League champions. After two seasons Flores in June 2013 left the Qatar. Three months later, he joined the Al Ain of the United Arab unitary, but was fired because of poor record in March 2014.
Flores ended less successful trip to the Middle East, returned home to Spain. January 2015 Flores coached the first team Getafe sent to invite them to just let go of the R & F coach Contra. But come back to the old Flores coached seven weeks only played one game after angrily to leave because he was dissatisfied with the team the midfielder Samir sale to Jiangsu Sainty.
In June 2015, Flores took over the newly-promoted Premiership Watford. While the success of the team in the British crown, in the dump is in turmoil over the past 12 months for the five coaches. The big boss to make critical satisfaction Pozzo was not easy, Flores accepted the invitation. Interestingly, three of the former Valencia coach finally gathered in the Premier League, and they are three consecutive terms of coach: Ranieri, Flores and Coleman.
Although the Spanish coach, Flores has always prefer flying in the traditional style of play as well as relying on two strikers attack, Waterford undoubtedly give him good resource. The team had two strikers Dini and Yi Haluo teamwork, rich in Pozzo family financial support of Flores can also bring some Spanish acquaintances, such as Juanfran and Jurado.
Failed to attract some high-priced star players or a young rookie, can only bring some not very young and experienced players strength, Flores can still manage a team, Watford under his leadership in early away relegation zone, three newly promoted this season to become the most have a hope of relegation. December, Flores led the team won four games of the month three games, won the best month. Activation good striker Flores also successfully activated Ignatius Harlow, who almost to super striker in the Premier League and tied for the two non Valdivia big scorer, but to occupy the top three people.