Aberdeen
Nicholson's performances at East End Park saw him signed by Aberdeen for a fee of £250,000 in July 2005 and re-joined former boss Calderwood who had since moved to Pittodrie. The move paid dividends as his strong performances towards the end of the 2006–07 season saw him score vital goals. The most notable of these goals was the last minute equaliser against Hearts, which all but clinched third place for Aberdeen, with only two matches of the season left at that stage.
In season 2006/07, the club finished in third place in the league and thus qualified for the 2007-08 UEFA Cup from which the Dons qualified from their group after a 4–0 win against F.C. Copenhagen. The Dons in the next round were twice ahead at home against Bayern Munich before drawing 2–2. The Bavarians won the return leg comfortably.
In October 2007, Nicholson scored the first hat-trick of his career, by scoring three goals against Inverness Caledonian Thistle in the quarter finals of the CIS Cup, with two of these goals being penalties.
Nicholson scored the 2nd goal for Aberdeen against Queen of the South in the 2007/08 Scottish Cup semi finals. Queens won the 7 goal thriller 4–3 to make it to the final for the first in their history. He later magnanimously said, "I think that they were the better team and deserved to go through."
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