Luton were docked 30 points for financial irregularities at the beginning of the 2008–09 season, and although Keane made 40 league appearances, primarily in midfield, he could not prevent the inevitable as Luton were relegated from the Football League for the first time in 89 years. Some solace could be found as Luton beat Scunthorpe United 3–2 in the 2009 Football League Trophy Final at Wembley Stadium, with Keane producing a superb performance in midfield. His displays earned Keane the Player of the Season and Internet Player of the Season awards for the second year in a row.