Jones was drafted to with their first selection and the 12th overall in the
2005 national draft. He made his debut against the in Round 17, 2006, at the
Melbourne Cricket Ground and played the remaining eight games for the season, including the elimination final win against and the semi-final loss to . After his fourth match, he earned the Round 20
Rising Star nomination for his game against the , where he collected 25 disposals. Jones remained a consistent figure in the side, playing every match in 2010 and 2011, including his 100th AFL game in the latter season. Jones established himself as Melbourne's leading midfielder in 2012 by winning his first
Keith 'Bluey' Truscott Medal as the club's best and fairest; in addition, he polled 14 votes in the
Brownlow Medal count to finish inside the top 20. He was named as vice captain prior to the 2013 season. In May 2013, Jones was appointed as interim co-captain alongside
Jack Trengove, replacing the injured
Jack Grimes. He played every match during the season and won the best and fairest for the second consecutive season, finishing ahead of
Colin Garland. After the appointment of new coach
Paul Roos, Jones was elected as co-captain alongside Jack Grimes for the 2014 season. He played every match for the season, amassing a career-high 610 disposals, the second-highest tally in the league during the home-and-away season, as well as having the fourth-highest number of clearances. He won his third consecutive Keith 'Bluey' Truscott Medal, a feat only previously achieved by club champion
Jim Stynes. At the end of 2014, Jones signed a four-year contract extension with the Demons, practically ensuring he would remain a one-club player. In February 2015, after Jack Grimes relinquished the co-captaincy, Jones was announced as sole captain, with
Lynden Dunn named as vice-captain. He played his 200th AFL game in the Round 22 match against ; however, he suffered an ankle injury in the second quarter that forced him to be substituted out of the game. He finished fifth in the best-and-fairest count; and, despite playing every match for the season, it was announced that he had played most of the season with a neck injury. In 2021, the 33-year-old Jones sustained multiple injuries (including a
hamstring and later
calf injury) that saw him missing the majority of his season (as in 2020, where he'd injured his
quadriceps). Nonetheless, Jones became just the second Melbourne player, after
David Neitz, to reach the 300-game milestone for the club, doing so against in round six. After Melbourne qualified for the
2021 AFL Grand Final, the injured Jones made the decision to return home to Victoria to be with his wife for the birth of their twins. He subsequently announced his retirement from the AFL, finishing on 302 games, four short of the club's all-time games record held by Neitz. == Coaching career ==