On 25 January 2009, Lescott scored Everton's only goal – a close-range header – in the FA Cup fourth round meeting with Liverpool. The match ended as a 1–1 draw, but Everton went through by scoring the replay's only goal in extra-time on 4 February. Lescott played for Everton in the 2009 FA Cup Final at Wembley Stadium on 30 May, resulting in a 2–1 defeat to Chelsea.
Following the end of the 2008–09 season, Manchester City attempted to sign Lescott, but Everton publicly rejected two offers from the club. On 11 August 2009, Lescott submitted a formal written transfer request, which was immediately rejected by Everton. Manager David Moyes refused a request from Lescott to be taken out of the squad for the first home match of the season, a 6–1 defeat to Arsenal. Lescott received a mixed reaction from Evertonians when the teams were announced on the PA system.
The ongoing saga finally came to an end when Lescott moved to Manchester City for a fee speculated to be £22 million with Lescott signing a five-year contract with the club on 25 August 2009. Lescott made his debut for City on 27 August in a 2–0 League Cup away victory over Crystal Palace and scored his first City goal in a 2–2 draw with Fulham on 25 October 2009. Lescott's first season and a half proved to be a frustrating time for the defender with him struggling to find the form he had shown at Everton, along with picking up a number of injuries, which included re-injuring his knee after hyper-extending it in a 3–3 away draw with Bolton Wanderers. Roberto Mancini replaced Mark Hughes as manager in December 2009 and preferred Lescott after his return from injury to Kolo Touré to partner the fast improving Vincent Kompany for a few months which in this time, including an impressive 4–2 win over Chelsea at Stamford Bridge in March 2010. With Lescott finally showing good form he would once again find himself frustrated after picking up another niggling injury, which would see him struggle to get back into the team in his preferred central defensive role for the foreseeable future.