Eastern Suburbs Moon took charge of Eastern Suburbs in the Brisbane Premier League Division 1 for 2008. In his first full year of coaching he took the club from 10th the previous year to champions, on the way making it to the Premier Cup Grand Final where they were beaten on penalties by
Peninsula Power.
Brisbane Strikers In 2009, Moon signed for the Brisbane Strikers in the Queensland state league.
Peninsula Power After securing the 2009 QSL champions medal, Moon signed for the 2009 Brisbane Premier League champions Peninsula Power.
Queensland Lions In 2012 Moon was appointed head coach along with longtime friend and player Scott Macnicol. At the end of the 2014 season he was offered head coach of Queensland Lions, where he once trained with the Queensland Roar.
Anglican Church Grammar School Moon also coached the
Anglican Church Grammar School First XI, with his last season at the school being in 2019. Warren Moon was head coach of the First XI at Anglican Church Grammar School. In 2019, he coached the school to their first
GPS Football premiership.
Brisbane Roar Moon left the school after accepting an offer to become the new general manager of the Brisbane Roar Academy in 2019. On 16 July 2020 the Roar appointed Moon to the A-League head coaching role replacing interim coach
Darren Davies after winning just 3 games in his 18 match spell. 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.
Central Coast Mariners Moon was appointed as the interim coach of the
Central Coast Mariners, a week out from the beginning of the
2025–26 A-League season, after the sudden departure of
Mark Jackson. ==Managerial statistics==