He scored once during his spell in Aberdeen, his strike coming in a 2–0 Scottish Cup win over his future club Livingston on 26 January 2002.

[8] It was in this spell at the West Lothian club that he regained his form and won a deserved call up from Berti Vogts for the International friendly match against Trinidad and Tobago.

In January 2006, McAllister agreed a two-year contract extension; however he was soon dissatisfied with his peripheral status at the club, particularly after the appointment of Valdas Ivanauskas as Hearts manager in April.

On 2 October 2008 McAllister was recalled to the Scotland squad by manager George Burley for the 2010 FIFA World Cup qualifier against Norway.

[15] Having been released by Bristol City at the end of the 2011–12 season, McAllister signed for Football League One side Yeovil Town on a two-year contract linking up with former manager Gary Johnson.

[21] On 2 October 2008, McAllister was recalled to the Scotland squad by manager George Burley for the FIFA World Cup qualifier against Norway.

[15] On 17 March 2009, McAllister was called up to the Scotland squad for their 2010 FIFA World Cup qualifying double-header against the Netherlands and Iceland.

[22][23] On 21 August 2014, while still an active professional footballer, McAllister joined Indian Super League club Kerala Blasters as a player/coach role where he would be the assistant manager under David James.

On 1 July 2016, McAllister announced his retirement from playing professional football to take up the role of under-21 manager at Bristol City.

[2] The following September, he was appointed interim head coach of the Brunei national team, taking charge of the Wasps for the play-offs for the third qualifying round of the 2027 AFC Asian Cup against Macau over two legs.