Caicedo scored his first goal for City the following season in a UEFA Cup game against Racing de Santander. He scored his second consecutive goal with a back heel in a league game against West Bromwich Albion, but the goal was initially ruled as an own goal, as it hit the post and then the goalkeeper before finally going in. The goal was later given back to Caicedo after reconsideration from the Dubious Goals Committee. After these solid performances, both coming off the bench, club manager Mark Hughes gave him the opportunity to start his first game in the league and he went on to score for the third game in a row, this time scoring the first two goals against Hull City on 26 December 2008, in a 5–1 victory, taking his goal tally up to four. He started against Blackburn Rovers on 28 December 2008. Caicedo opened the scoring in the first leg of the UEFA Cup last 16 tie with Aalborg BK at the City of Manchester Stadium. Manchester City won the game 2–0. Caicedo scored his sixth goal of the season for Manchester City against Hamburger SV on 16 April 2009, but City were eliminated from the cup 4–3 on aggregate. Caicedo impressed many Manchester City fans that season with his strong performances as a single striker with the ability to hold up the ball in key areas and shrug off defenders. Caicedo's seventh City goal came in City's 3–1 home win over Blackburn Rovers on 2 May.