Silvagni spent four years at the club as defensive coach, leaving at the end of 2010 to work with Greater Western Sydney, while Elshaug became head of recruiting.

Other notable assistants to have worked with Lyon in his time as coach include Leigh Tudor and Robert Harvey.

[7] Lyon began his first season as senior coach with a victory against Melbourne in Round 1 of 2007 and the Saints then won four of their first seven games.

Injuries hit the club badly in Round 8, however, with St Kilda having only 24 out of a possible 38 players to choose from against Hawthorn.

Lyon was criticised for flooding excessively and many became angry with the more defensive style of St Kilda over the subsequent weeks.

This left the Saints in eighth position on the ladder, a spot the side was unable to maintain after narrow losses to reigning grand-finalists Sydney and West Coast in the remaining five rounds [1].

The team narrowly missed playing finals for the fourth consecutive season, finishing 9th with 11 wins, 10 losses and 1 draw for the year.

[10] St Kilda started the season strongly by winning the 2008 NAB Cup, defeating the Adelaide Crows by five points at Football Park.

In the second half of the season, their fortunes improved sealing a spot in the top four with a record-breaking 108-point victory against Essendon in the final round.

Over the pre-season Lyon worked on a new game plan based around forward pressure, midfield zone defence and pushing numbers behind the ball.

[13] Despite losing narrowly to Essendon and North Melbourne late in the season, the Saints finished two-games clear on top of the AFL ladder, winning the McLelland Trophy for the first time since 1997.

Lyon became only the third coach (after Stan Alves and Allan Jeans) to lead the club to a grand final since World War Two.

St Kilda led the game at every quarter but fell short at the final siren, losing the match by 12 points.

Lyon became the only coach apart from Allan Jeans to lead St Kilda to multiple grand final appearances.

St Kilda then started their revival, defeating Melbourne in Round 9 and then only losing three more games for the remainder of the year.

[26] After starting the 2012 season strongly with a 5–2 win–loss record, including wins against reigning premiers Geelong and Lyon's former club St Kilda, Fremantle struggled in the middle parts of the season, highlighted by big losses to Hawthorn and cross-town rival West Coast.

The Dockers finished seventh in the regular season and defeated Geelong in their elimination final match to advance to the semi-finals, where they subsequently lost to Adelaide.

[32] In October 2022, following a disappointing end to the 2022 AFL season, St Kilda sacked incumbent senior coach Brett Ratten and immediately made overtures to Lyon about a possible return.

[33] Lyon's return to St Kilda was confirmed with his appointment as senior coach on 24 October for a second stint[34] to a four-year deal.

Having remained in the top eight all season, the Saints under Lyon finished the 2023 season in sixth place on the ladder with the best defence in the competition, conceding an average of only 71.6 points per match, but with the fourth-worst attack (and worst of any of the top eight sides), scoring an average of only 77.2 points.

[43][44] Lyon has also been criticised, including by former St Kilda coach Scott Watters, for sticking to his game plan at the expense of having an effective forward structure.

[51] Despite an internal investigation that cleared him, the woman felt harassed, humiliated and intimidated by unidentified Fremantle football club staff, leading to her resignation.