In the latter years of his playing career, Wise gradually became involved in the managerial aspects of the game, starting at Millwall, where he took on the role of player-manager, taking them to the FA Cup Final and European football for the first time ever. He was briefly caretaker manager at Southampton, following the departure of Harry Redknapp, before he took over the reins at Swindon Town on a permanent basis. In October 2006, he was appointed manager of the then-Championship side Leeds United, who found themselves in the relegation zone. Although they were ultimately relegated, Wise reshaped his side in the close season and Leeds made an excellent start to their first season in the third tier of English football.