Finals Misses: 2005–2008
The Lions had an inconsistent season in 2005 and fell away badly towards the end, losing many games by very large margins. This culminated in a record 139-point defeat at the hands of the St Kilda, whom they previously defeated in Round 1 in a controversial encounter. They finished a disappointing eleventh – out of the Finals for only the second time in the club's history. When able to field its strongest lineup, the Lions produced some strong performance reminiscent of its triple Premiership days. However, injuries to Justin Leppitsch, Jonathan Brown, Nigel Lappin, and the retirements of Premiership players such as Marcus Ashcroft, Alastair Lynch, Martin Pike, Shaun Hart and Craig McRae had taken its toll and the club played more first year players than any other side in the competition.
The Lions began the 2006 season optimistically, but injuries again plagued the club, whose players recorded an AFL record total of 200 matches lost to injury for the season.
Justin Leppitsch was forced to retire through injury and with season ending injuries to prominent players Nigel Lappin, Chris Scott, Ashley McGrath, Richard Hadley, Anthony Corrie and key ruckman Jamie Charman. Coach Leigh Matthews was forced to debut an unprecedented number of youngsters and rookies and due to this, the club experienced inconsistent results. While many of the new youngsters displayed great promise, and continued to attack the ball and tackle opponents in typical Brisbane Lions spirit, it became evident during the final few matches that the young Lions were clearly into rebuilding mode. With AFL Rising Star nominations to Michael Rischitelli, Cheynee Stiller and Matthew Moody, and the emergence of rookie Jason Roe among others, the future looks promising, but the realists also know that the rebuilding phase will take a few years.
Despite the young team losing more home games than ever before, and reducing the Gabba's status as a fortress that intimidated opposition teams, the Lions still produced average crowds the equal of the NRL Premiership team Brisbane Broncos.
Justin Leppitsch and Brad Scott announced their retirements during the season. A controversial and high-profile feud between the club and Jason Akermanis divided supporters of the club and received massive publicity, resulting in Akermanis being stood down for the last seven matches of the season by his senior playing peer group, who felt that his loyalty to the club and playing group was compromised.
After the 2006 home and away season it was revealed that major sponsor AAPT would not be renewing their sponsorship. It was announced shortly after that Vodafone had signed a sponsorship deal with the club worth A$5.4 million over three years.
The Brisbane Lions team of the decade fullback Mal Michael announced his retirement from football on 5 October 2006 due to lack of motivation and desire to pursue other non-football related activities. While at the Lions he was one of the premier fullbacks in the AFL and was somewhat unlucky not to receive an All-Australian honour and was a pivotal figure at the Brisbane Lions, playing a significant role in each of the grand finals contested. In highly controversial circumstances, a contract loophole enabled Michael to sign with the Essendon Bombers and continue his career there.
The captain, Michael Voss, also announced his retirement from football on 6 October 2006 due to the stress placed on his body from years of football and a chronic knee injury. He was the co-captain of the team from 1997 to 2000 with Alastair Lynch before leading the side for the remainder of his career, including the historic three straight premierships. In his final season of football, Voss still played 21 out of a possible 22 games, missing one game through knee soreness which turned out to be the same knee which led to his retirement.
At the completion of the 2006 season Chris Johnson remained as the last ever representative of the Fitzroy Football Club to be playing senior AFL football.
The Brisbane Lions finished runner up in the 2007 NAB Cup and then went on to create history by being the first team in the history of the AFL to have five co-captains. They started the season with a convincing 25 point win over Hawthorn, 9.15.(69) to 6.8.(44) and a massive win, after tributes to former captain, Michael Voss, against the St Kilda Football Club, with a 52 point margin.
On 12 May 2007, the Lions marked Leigh Matthews' 200th game in charge of the team against the Crows
One week later, on 19 May 2007, against Mal Michael's new team, the Essendon Bombers, the Lions began confidently but eventually succumbed to their biggest loss in season 2007 by a margin of 64 points. The Lions lost to Collingwood by 33 points at the Gabba in Round 9 and drew with Richmond at Docklands Stadium with the final scores 10.13 (73)apiece.
On 7 June 2007 Lions co-captain Simon Black and former Lions captain Michael Voss were charged for an assault that allegedly took place on the eve of the 2006 AFL Grand Final. Against Jason Akermanis's new side, the Western Bulldogs, in Round 11, the Lions yet again began confidently, kicking the first two goals of the game before being overrun. The Lions failed to score a goal in the second quarter but came back in the last to reduce the margin to 23 points, holding the Bulldogs goalless in the final term. Akermanis kicked two consecutive goals in the first quarter to take the margin out to 15 and 21 points respectively.
At a rainy Kardinia Park two weeks later, the Lions failed to score a goal in the first half and never looked like coming back, going down to their second biggest loss of the season so far. On 30 June 2007, Brisbane faced Port Adelaide and led by seven points at quarter time before being overrun in the second, the Power kicking seven goals to two to led by 19 points at half-time. At three-quarter time, the Lions were down by 28 points and 40 points a few minutes early into the final term before they fought back to level the scores at 105-all courtesy of a Jonathan Brown goal from a free kick. A minute later a 50-metre penalty gifted Port Adelaide's Brett Ebert a goal and managed to hold on for a seven point win.
On 22 July 2007 the Lions faced a struggling Carlton Blues side who were on the back of a 62-point thrashing to Sydney the previous week. Brisbane kicked 8.5–0.3 in the last quarter, the final margin being 117 points, Brisbane's biggest ever win over Carlton, bettering their 103-point loss to Carlton in Round 10, 1987. Also, gun forward Jonathan Brown became the first player in Brisbane Lions/Brisbane Bears history to kick 10 goals in a match, beating Brad Hardie (1989) and Daniel Bradshaw (2005) who both kicked nine goals. This resulted in the sacking of the opposition coach after a run of poor results.In Round 17, the Lions celebrated their return to the Melbourne Cricket Ground with a 93 point defeat of Collingwood. Jared Brennan played one of the best games in his 54 game career, scoring seven goals and five behinds.
Rhan Hooper received a three match ban for striking Hawthorn's Rick Ladson, Joel Macdonald and Troy Selwood missed the must-win clash against Sydney. Brisbane started off well with Richard Hadley booting the first goal of the game but poor kicking and too many turnovers saw them trail by 10 points at quarter-time before Jonathan Brown evened the scores at 24-all at half-time. The Lions failed to score a goal in the third time-scoring 0.3 to the Swans' 3.5. However, they jumped straight out of the blocks in the first 3 minutes, with Jonathan Brown putting the Lions in front with his second for the night. But with less than four minutes remaining, Brett Kirk thought he'd won the game for Sydney only for Jonathan Brown to kick a 55-metre goal just before the full-time siren to secure a 9.9 (63) to 8.15 (63) draw.
The Lions failed to make the finals for a third successive year and lost Chris Johnson and Chris Scott to retirement. Youngster Cameron Wood was traded to Collingwood in exchange for Pick 14, which the Lions gave to Melbourne for Travis Johnstone. On the last day of the 2007 trade week, Richard Hadley was traded to Carlton for pick #52.Simon Black and Jonathan Brown are two of the Lions' Premiership players still playing at the club
The Lions began the 2008 NAB Cup shakily, losing to Essendon by 27 points. The 2008 home and away campaign started with a game against the West Coast Eagles at Subiaco Oval, in which the Lions lost by 16 points. In their second match at home at the Gabba, the Lions wrestled with an in form Collingwood and eventually triumphed by two points. Jed Adcock scored the winning goal for the Lions. After a 17-point loss to the Sydney Swans the next week (Rivalry Round), the Lions managed a record breaking comeback against Port Adelaide after turning around a 47-point deficit half way through the third quarter, to come out winners by 20 points by the final siren. The Lions were then defeated by Hawthorn by 12 points followed by a sound victory over Melbourne by 52 points. They suffered another defeat to Geelong by 27 points followed by the Lions' first consecutive wins for the season with wins over Carlton by 33 points and St Kilda by 46 points. This was followed up by wins over North by 31 points and Fremantle by 22 points. The winning streak would eventually be snapped by a defeat from the Bulldogs by 63 points. The team struggled for the rest of the season and missed out on the finals with a 10–12 record, losing 3 games despite having at least 5 more scoring shots in each of those games. Coach Leigh Matthews resigned at the end of the season after 10 seasons and 3 premierships with the club.