Born in Canelones Department, Flores moved to the capital of his country, Montevideo and began his football career at Club Atlético River Plate,.

[3] On 10 August, he debuted in a 1–1 draw with Colón de Santa Fe at Estanislao López for the first week of the Apertura Tournament, in which Flores scored the equalizer for his team in the 54th minute.

On 11 June 2010, it was confirmed that he joined to Uruguayan Primera División powerhouse team Club Nacional de Football in a one-year deal, along with Mariano Pernía, the former left back of Atlético Madrid.

He had a very regular first season with Nacional, playing only seven games since his incorporation during the Apertura Tournament, and was red carded for first time in his career in a 2–1 home win over Danubio at Estadio Parque Central.

Flores was frequently used as left midfielder by Juan Ramón and began to win a place in the team's starting lineup, proclaiming after champion of the Clausura Tournament.

[10] Flores debuted for the club based in La Cisterna, for the first week of the Apertura Tournament on 30 January 2012, in a 2–1 loss with Universidad Católica at the Estadio Nacional, in where he was the key player of his team, having a very high performance,[11] being again compared with Enzo Francescoli like when he played in Argentina with River Plate, but now by TVN journalist Fernando Solabarrieta at 24 Horas Central.