During Arsenal's pre-season campaign ahead of the 2008–09 season, Clichy captained the team for the first time in its 2–1 win over Barnet. He remained a fixture within the starting eleven during the season despite the emergence of youngster Kieran Gibbs. On 1 November 2008, Clichy scored his first professional goal in a 2–1 defeat to Stoke City. After consistently appearing with the team for the majority of the campaign, in April 2009, Clichy began missing matches due to an unspecified injury. After being sidelined for several weeks, it was announced in early May that the defender would miss the remainder of the 2008–09 season due to a back injury. Similar to his foot injury three seasons ago, during the high note of the 2009–10 season, Clichy's back injury relapse after it was revealed that the player suffered a stress fracture of the lower back in the team's 3–0 win over North London rivals Tottenham Hotspur. Despite being initially ruled out for a month, Clichy missed ten weeks and returned to the team in January 2010. He appeared in all of the club's remaining matches excluding one.