The 2013 season was initially a good one for Hird and the football club, during which the team was second on the AFL ladder with a 13–3 win-loss record after 17 rounds. However, internal pressure on the club finally took its toll on the players and coach when the AFL banned Essendon from participating in the 2013 finals series. The club on-field performances fell away and lost five of their last six games. In August 2013, he was suspended from coaching for 12 months when he was charged by the AFL with conduct prejudicing the game in relation to his role in the Essendon Football Club supplements controversy.
In April 2013, Hird, as coach, was accused of being personally injected with supplements in 2011 and 2012 that would be deemed performance enhancing if he were a player. Essendon players from 2011 and 2012 were also accused of ingesting performance enhancing supplements. As head coach, Hird was subsequently implicated.
Following months of rumours and investigations, on 13 August 2013, Hird, along with the Essendon Football Club, senior assistant coach Mark Thompson, football manager Danny Corcoran and club doctor Bruce Reid, was charged by the AFL with bringing the game into disrepute in relation to the poor governance of the supplements program at the club in 2011 and 2012. The club was given 14 days to consider the charges and faced an AFL Commission hearing on 26 August 2013.
On 27 August 2013, following much negotiation, Hird accepted charges that he had brought the game into disrepute and abandoned possible Supreme Court action against the AFL and its chief executive, Andrew Demetriou. He maintained that he did little wrong, but said he should have known more about the club's supplements program. He was banned from working at any AFL club in any capacity for twelve months commencing from 25 August 2013. Hird was allowed to attend Essendon matches as a spectator during this period. However, despite not being allowed to pay him for working as a coach during 2014, the club paid Hird $1 million in advance for 2014 in December 2013.
A media report on 3 October 2013 said that Hird denied pleading guilty for a reduced charge as alleged by Demetriou. Hird's lawyer, Steven Amendola, asserted that the AFL withdrew all charges against Hird under the deeds of settlement that he and the club signed with the AFL. At the time of the media report, Hird was considering legal action against both the AFL and Demetriou.