In his first year as Wigan's coach Maguire won the 2010 Super League Grand Final. In his second year he won the 2011 Challenge Cup and was signed by the Rabbitohs. In his first year as an NRL head coach he took the Rabbitohs deep into the 2012 finals series. In 2013 the Rabbitohs finished the regular season in second place and in 2014 they won their first premiership in 43 years.
Maguire did not feature again until 1994 when he came off the bench again against Penrith Panthers. He had a more consistent season the following year, making six appearances in total, most of which he started as either Wing or Centre. Maguire's first try came as a centre against the Parramatta Eels.
In 1997 Maguire left Canberra and signed for the new Adelaide Rams club of the breakway Australian Super League competition. He made his début at fullback in the Rams inaugural game against the North Queensland Cowboys in Townsville which Adelaide lost 24-16. Maguire also participated in the World Club Challenge for the Rams that year. He went on to play four more games for Adelaide and scored one try before returning to Canberra in 1998. Maguire made two appearances for Canberra in 1998 before retiring after persistent neck problems.
When Maguire retired from playing rugby league he initially left the game and taught Physical Education before signing as a Strength & Conditioning coach for Canberra and later became assistant coach for the Canberra Raiders reserve grade under Mal Meninga. Maguire was eventually promoted to assistant coach of the Canberra first team alongside Matthew Elliott before leaving the club in 2004 to take the assistant coaching job at Melbourne Storm under former Raiders teammate, Craig Bellamy.
Maguire was an integral part in Melbourne's stripped NRL grand final victories and took control of first team affairs when head coach Bellamy took up representative duties for the Blues in State of Origin. This earned him plaudits from senior coaches in the NRL and Maguire was linked with a move to Brisbane Broncos as head coach in 2008. He was heavily linked with a move to English club Wigan Warriors towards the end of the 2009 season and signed a three-year deal with the Super League side on 7 October 2009.
Maguire started his Warriors coaching career with a victory against Crusaders in his first home match of the season. He ended the Halliwell Jones hoodoo against Warrington Wolves in a thrilling match which Wigan won 22-20. He won RLW coach of the month for February. Maguire then recorded his biggest victory as a Wigan coach, beating nearest rivals St Helens in the last ever Good Friday derby match at Knowsley Road. He and his assistant Shaun Wane helped guide Wigan to the League Leaders Shield in 2010. This was the first time Wigan topped the table in 10 years and marked a trophy winning start to "Madge's" Wigan coaching tenure. Maguire guided Wigan to their first Super League Grand Final appearance in 7 years as the Warriors beat Leeds Rhinos at Headingley by a scoreline of 26-6 on 25 September 2010. Maguire was crowned Coach of the Year 2010 at the annual Super League 'Man of Steel' awards dinner. 
In the 2014 NRL season, Souths were tipped to be winners of the minor premiership, along with the Sydney Roosters and Manly-Warringah Sea Eagles. The first finals round saw Souths defeat the Sea Eagles, then facing the Roosters in the preliminary final. Unlike the last round of the ordinary season, the Rabbitohs overcome an early 12-0 deficit to score 32 unanswered points, eventually winning the match 32-22. Under Maguire's coaching this was the first time since 1971 that the Rabbitohs had reached a Grand Final. The Rabbitohs defeated the Canterbury-Bankstown Bulldogs 30-6 in the 2014 NRL Grand Final, securing their 21st premiership.