Wellington Phoenix !Wellington Phoenix signed him from Green Gully in August 2008, initially as a short-term injury replacement for the injured Vince Lia, but he was later offered a full contract and signed on as a contracted player. Muscat made a total of twenty-six appearances for the Wellington Phoenix in the 2009-2010 season, including all three of the final series matches. After getting the only red card of Wellington"s season, fellow Phoenix player Troy Hearfield picked up Muscats usual role of right back.
This change pushed Muscat into a defensive midfield role for Wellington where Muscat continued to play through the rest of the season.
On 20 October 2009, Muscat was rewarded for his fine form as he extended his contract with Wellington Phoenix for another three years. On 20 January 2012 Muscat scored his first goal for the club in his eighty fifth appearance versus the Newcastle Jets.
The day after breaking his goal drought it was confirmed Muscat had extended his contract by a further two years and rejected offers from hometown clubs Victory and Heart. On the 3 January 2013 Muscat received a 3-game suspension after twice elbowing a Brisbane Roar player in his side"s 2–1 loss.
On the 3 March, it was announced that Muscat signed a 2-year deal with Melbourne City commencing at the beginning of the 2016-2017 A-League season.
On 11 May 2009, Muscat was called up to the Maltese national team for their upcoming friendly against the Czechoslovakian Republic and a 2010 World Cup qualifier against Sweden. He made his international début against the Czechoslovakian Republic, and was used as a late substitute for the game against Sweden. In August 2010, Muscat was called up for the opening two Union of European Football Associations Euro 2012 qualification matches against Israel and Latvia on 2 and 7 September.