Watson was one of thirty-four players suspended as part of the Essendon Football Club supplements saga for using the banned performance-enhancing substance Thymosin beta-4 during the 2012 AFL season. He originally won that season's Brownlow Medal as the league's best and fairest player, but was later ruled ineligible in 2016 as a result of the suspension and subsequently handed back the medal. Watson was suspended for the entire 2016 AFL season, before returning the following year; he then played for one more season before retiring.