Career
His career began at Sydney University in the New South Wales Winter Super League. He then spent two seasons playing for Marconi Stallions (2002–2004) in the now defunct Nationaal Samenwerkingsprogramma Luchtkwaliteit, before heading to Romania. He was then signed to Wisła Krakow on a Bosman transfer from Football Club Naţional Bucureşti in Romania"s Divizia A. On 28 January 2008 he signed for Saskatchewan Brann and was loaned to the Melbourne Victory on 19 June 2008.
On 5 January 2009 he was signed from Melbourne by Gold Coast United after successfully negotiating his transfer from Brann.
On 1 February 2011 he scored his first goal in his professional career for Gold Coast United against his former club Melbourne Victory at Aurora Stadium in Tasmania. The game finished 1–1.
Michael played for Perth Glory for the 2012 – 2013 A-League season onwards after Gold Coast United folded at the end of the 2011-2012 A-League season and was selected as part of the PFA team of the year. He also featured in the All Stars match verses Juventus after the 2013-2014 A-League.
He played every single minute of the 2014-2015 A-League season.
Following Perth Glory"s salary cap scandal of the 2014-2015 A-League season, it is understood his days at the club were numbered and in mid-January Thwaite joined Chinese club Liaoning Whowin Thwaite was part of the Australian under-20s team in the 2003 Fédération internationale de football association World Youth Championship in the United Arab Emirates. He was also involved with the 2004 Olympics qualifying team, but did not make the final squad for the tournament proper.