He made his debut against Richmond in Round 4 of 2005 when Matthew Carr was a late withdrawal from the team due to illness.
Due to promising performances at both WAFL and AFL levels and his versatility, he announced a three-year extension to his contract in 2006[2] and then a two-year contract extensions to remain at Fremantle until the end of the 2011 season.[3]
In 2006, Michael finished equal runner-up (with Peter Bell) in Fremantle's Doig Medal Best & Fairest count, further underlining his credentials as a prospect for the future.[4]
His 2007 season started badly when he was suspended for four matches after colliding with Lachlan Hansen in a NAB Cup match and being one of the first players to be charged under the AFL's crackdown on front-on contact to the head.[5]
In 2009, he was appointed captain of the club for a pre-season derby[6] and despite missing the second half of the 2009 season due to an ankle injury,[7] he was officially included in the leadership group for the 2010 season. He also won the club's best clubman award for 2009.[8]
In May 2010 Johnson was investigated by the police in relation to a drug-related matter.[9][10] He was charged on summons with possessing cocaine, suspended for five matches and fined $5,000 for bringing the AFL into disrepute. He pleaded guilty and was fined $500 in court.[10][11][12]
In November 2016, Police investigated Johnson after it was alleged that he punched a Bunbury School teacher in the face while intoxicated at a kebab shop in Leederville.[13] He was found guilty and fined a total of $4500, but was given a spent conviction.[14]
In 2017, Johnson was integral in Fremantle's early season turnaround assisting Aaron Sandilands in the ruck despite the team generally taking a youth first approach in their team selection criteria.[15][16]
Johnson retired at the end of the 2018 season.[17] In February 2019, he was appointed as Fremantle's inaugural indigenous and multicultural liaison officer.[18]