In the 1999 National AFL Draft, Bowden was a fourth-round selection (no. 58 overall) to the Western Bulldogs. With limited opportunities at the Bulldogs, he was traded at the end of the 2005 AFL season to the Richmond Football Club in return for the 55th pick in the 2005 AFL Draft, which the Bulldogs used to select Brett Montgomery.
In the 2006 AFL season, Bowden had his best season to date. He led Richmond's list for marks and was equal fourth for marks in the competition.
After a year full of injury and poor form, the Tigers delisted Bowden at the end of season 2007.