Maitland was appointed successor to Tom Hendrie as Alloa Athletic manager on 9 January 2006, with Alloa sitting eight points adrift at the bottom of the Scottish Second Division. Maitland's first game in charge of Alloa was not an easy game, a midweek Scottish Cup Third round replay away to SPL opposition, Livingston. Alloa fell behind to a Paul Dalglish penalty before half time but rallied in the second half with great goals from Robert Sloan and Ross Hamilton to win 2-1. Maitland then needed to turn this kind of gritty performance to the league to save Alloa from relegation. He managed to steer the club to a ninth place finish meaning entry into the playoffs to decide relegation from/promotion to the Scottish Second Division. Alloa met Arbroath in the semi-final where they won through 2-1 on aggregate. This meant a play-off final showdown with Berwick Rangers. Alloa basically put the tie out of Berwick's reach with a 4-0 home win in the first leg which was following by a 2-1 Berwick win in the return fixture ensured Alloa's Second Division future.
In Maitland's first full season in charge at Alloa, the club finished in seventh place which was followed by a clear out of 10 players with Allan quoted as saying "I want this club to be looking up the way and looking to challenge at the right end of the division next season, to do that there needs to be radical surgery and by releasing these players tonight it creates space for other players to come in..." Maitland has started to build his squad for the 2007-2008 season with the addition of nine new players including experienced defender Derek Fleming and second time Alloa midfielder Brown Ferguson.
Maitland was sacked in May 2011 following the club's failure to avoid the relegation playoffs.