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 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.