[2] After a troubled time, with small crowds, confronting relegation and with a "disenchanted team", former Australian Soccer Federation chairman Ian Brusasco headed a trustee management group to restructure the club.

Coached by Stowell for three seasons, the Strikers finished fourth in 1995/96 to qualify for their first NSL finals appearance, in which they lost a semi-final playoff over two legs to Sydney United.

In the 1996/97 season, the Strikers ditched the white to wear a predominately gold kit, with blue trims, and were led by player-coach Frank Farina.

But the 1997 Grand Final, played at Lang Park in Brisbane, drew a capacity 40,446 spectators to watch the Strikers beat Sydney United 2–0 with goals by Farina and Rod Brown.

"[7] Public pressure eventually convinced Soccer Australia to reverse its decision and grant the Strikers Football Club Pty Ltd a licence for the 2000/2001 season.

Together, the two assembled a squad of unsung players from the local leagues and turning them into a team that took the club back to the 2003/04 NSL finals only to lose a memorable semi-final play-off to Adelaide United.

Football Federation Australia boss Frank Lowy was quoted at the time saying that the two Brisbane bids were outstanding [citation needed], but the reality was that only one team would make it.

Its application to join the new state competition was accepted and the club, once again under the coaching of Stuart McLaren, put its best foot forward on playing fields from Brisbane to Townsville in the inaugural QSL season.

The following (2009) season, McLaren and his squad clinched the QSL championship in the penultimate round of the competition after a tense season-long battle with Olympic FC.

However, the Strikers lost in a Grand Final once again, going down 1–4 in a boilover result to Redlands United FC, who had finished the season in fourth position on the QSL ladder.

With David Large taking on the coaching role from the departing McLaren, the club finished both seasons in second position on the league table before going on to host the Grand Finals and losing each one by an identical scoreline, 1–0 to Sunshine Coast FC.

The Strikers claimed their second QSL championship in five years in emphatic fashion, finishing eight points above second place Far North Queensland Bulls FC.

With the Strikers equal top of the league but second on goal difference their final game of the season was abandoned due to wet weather and with the governing body, Football Queensland, choosing not to reschedule the match and deem it a goalless draw they were forced to settle for the runners-up position.

The disappointment from the last game controversy was further heightened when the Strikers qualified for the Grand Final, only to lose to their league rivals Moreton Bay United.

The following year, an annual $500,000 bequeathment from the late Dr Jones, which was paid to Strikers, Sport, Recreation and Welfare Association Limited for a decade after his death, ended as per the terms of his will.

The club's 2020 financial report, submitted to the Australian Securities and Investments Commission, noted: "The discontinuation of the above funding subsequent to 30 June 2018 gives rise to a material uncertainty which may cast significant doubt about the ability of the entity to continue as a going concern.

[12] For the 2021 season, and without the financial stability of Dr Jones's bequeathment, Strikers chairman Bruce Atterton-Evans announced a new youth-focused policy[13] that saw almost the entire first-team squad depart for rival clubs.

Atterton-Evans ceased being a director on 14 October 2021,[14] leaving the Strikers under the control of Sottile, Suranyi and Bosnian-born Brisbane businessman Dino Hasanovic.

Qualifying through the Brisbane zone for the national Round of 32 in 2014 the Strikers featured in a piece of Australian football history when its tie against Newcastle based club Broadmeadow Magic became the first live televised game of the new Cup competition.

[20] The Strikers qualified for the quarter-finals for the very first time on 29 August 2019, when they defeated Manly United 1–0 in front of 1240 spectators at Perry Park[21] and drawing Moreland Zebras in the next round.

The Strikers defeated the Zebras 3–2 in front of 1915 at Perry Park on 18 September 2019,[22] to become the first Queensland side to qualify for the FFA Cup semi finals, setting up a match with Melbourne City.