With Gaël Clichy injured and Ashley Cole absent from the team due to his protracted transfer to Chelsea, Hoyte began the 2006–07 season as Arsenal's temporary left back, starting against both Dinamo Zagreb and Aston Villa, although this was expected to be a temporary measure. When Clichy recovered, Hoyte moved back to his preferred right side of defence to cover for the injured Emmanuel Eboué. Hoyte scored his first goal for Arsenal on 2 January 2007 in a 4–0 defeat of Charlton Athletic, which made him the first Englishman to score for the club in their new Emirates Stadium. He finished the season with 36 appearances, a total that included a starting place in the League Cup final, which Arsenal lost 2–1 to Chelsea.