He returned to Scotland in season 2005–06 with Aberdeen. In August 2005, Smith struck a late winner as Aberdeen defeated rivals Rangers in a league match for the first time since April 1998, wowing the Aberdeen support in only his third competitive game for the club. He was involved in a car crash along with teammate Michael Hart in July 2007, while on a pre-season tour of Egypt. Smith was treated for concussion, while Hart was unhurt.
In December 2007, Smith played a key role in Aberdeen's victory over Danish team FC Copenhagen in the 2007–08 UEFA Cup, scoring two goals in the 4–0 victory that saw Aberdeen through to the last 32 of the competition. Smith's contract at Aberdeen ended at the end of the 2008–09 season and he expressed concern that he had not been offered a contract extension, stating that he may need to look for a new club in summer.
In May 2009, he was given permission to discuss a contract with Major League Soccer side Toronto FC. However, Toronto passed on the signing of Smith and he later signed with Colorado Rapids in July 2009. In his first season with the Rapids he played only four games before suffering a season-ending knee injury.
On 28 August 2010, Smith scored his first MLS goal two minutes into a match against Houston in which he was named man of the match.