Moon then returned to Australia after struggling with injury and signed as a coach/player for Brisbane Premier League First Division team Eastern Suburbs in 2008.
Warren Moon was head coach of the First XI at Anglican Church Grammar School.
[5] Moon left the school after accepting an offer to become the new general manager of the Brisbane Roar Academy in 2019.
[7] Moon was sacked by the club on 20 February 2023 after a 1–1 draw with Sydney FC that extended the team's run without a win to 7 games and left them in 2nd last place on the table.
His final statistics as Brisbane manager were 22 wins, 22 draws (29% respectively) and 31 (41%) losses, qualifying for the A-League finals twice & being knocked out in the first week both occasions, and a highest finish in the Australia Cup of the semi-final in the 2022 edition, losing 3-2 to NPL team Sydney United.