After a regular pass in Argentina, he completed his loan spell with River Plate, and moved to La Liga side Villarreal, days later of his last game for River against Godoy Cruz. On 25 June 2009, Flores was officially presented in the club based in town located at Valencian Community, however he accepted his role in the reserve team, Villarreal B that play in the Liga Adelante, being also confirmed that he would play some games with the first team. On 29 August 2009, Flores made his club debut in a 2–2 home draw with UD Levante at El Madrigal Stadium. During the season he played one goal in 24 appearances with the team, but failed to play games with Villarreal in the 2009–10 season of the Spain's Liga BBVA, because the coach Juan Carlos Garrido not considered him in the first team. 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. Flores made his debut in a 1–1 away draw with Montevideo Wanderers at Centenario Stadium. 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. During the season, was not considered by the coach Juan Ramón Carrasco, who directed him during his successful pass at River Plate Montevideo, due to his lack of form. The next season, he played his first Copa Libertadores game with Nacional in a 2–0 away defeat against América at the Estadio Azteca. 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. After the sorpressive departure of the coach Carrasco, and the also sorpressive arrival of his teammate Marcelo Gallardo as coach, he was not considered by him and weeks later, Flores moved to Bulgarian First Division side Litex Lovech.
On 24 December 2011, Flores joined to Chilean Primera División club Palestino, in where play his brother Darío. He joined in a free transfer and signed a one–season contract that will keep him until December 2012, being also named as the best signing of the tournament on 28 January 2012 according to the web site of La Tercera newspaper. 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, 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. His first goal in the Chile came on 24 March against Audax Italiano in a 2–1 away win at the Estadio Bicentenario de La Florida for the fifth week of the tournament. Another good game of Flores in the season was against Colo-Colo at the Estadio Monumental on 25 March, in where his team won of incredible form 1–0 with tremor inclusive. During that game, Robert collaborated very much for his team that is directed by his compatriot Daniel Carreño, his major input was his assist in the moment of the goal.
