He played his first game back from injury against Arsenal in the FA Cup sixth round on 12 March 2011. On 9 April 2011, he scored his first league goal of the season as he netted the second of a 2–0 home win over Fulham. Days later, he scored the first goal in United's 4–1 victory against the German team Schalke 04 in the second leg of the semi-final of the 2010–11 UEFA Champions League, game in which he was selected as player of the match. He became the first Ecuadorian player to win a Premier League medal, in the 2010–11 season. Valencia was a starter in United's 3–1 defeat to Barcelona in the 2011 Champions League Final at Wembley Stadium.
On 1 August 2011, Valencia agreed a new four-year deal with Manchester United, keeping him at the club until the summer of 2015. Prior to the start of the 2011–12 season, Valencia picked up an ankle injury on international duty with Ecuador at the Copa América during the summer. He missed United's entire pre-season tour of the United States because of the injury. He also missed the first month of the season because of a lack of match fitness. Valencia made his first start of the season away at Benfica in the first group stage match of the UEFA Champions League. On 18 September 2011, he returned to Premier League action, replacing the injured Chris Smalling at right-back in the 3–1 win against Chelsea. He then continued to play right-back in the next three games against Leeds United in the League Cup, away at Stoke City, and home against Norwich City in the Premier League. Valencia scored his first goal of the season, in a fourth round League Cup tie against Aldershot Town, receiving the ball in the middle of the park and then turning and firing in from 25-yards to seal a 3–0 victory.
Valencia scored his second goal of the season, the opening goal in Manchester United's Champions League fixture against Oțelul Galați. The game finished 2–0. On 26 December 2011, Valencia scored the fourth goal for Manchester United in a 5–0 home win against Wigan Athletic. He received the ball on the right hand edge of the penalty area and rifled a shot across goal and into the far corner. On 22 January 2012, Valencia scored the first goal against Arsenal with a header, before later setting up Danny Welbeck to win the game 2–1. On 2 April 2012, in his 100th appearance for the club in all competitions, Valencia scored the first goal in a 2–0 win against Blackburn Rovers, powerfully curling the ball around Paul Robinson and inside the far corner. Five minutes later, Valencia set up the second goal for Ashley Young.
On 3 July 2011, in a match against Paraguay at the 2011 Copa América, he suffered a sprained left ankle and was forced off at half-time.