In 2012, Dandenong claimed the famous treble of the Victorian Premier League Minor Premiership, the Football Federation Victoria State Knockout Cup and the VPL championship.

[1] The club sometimes had the additional name Prishtina added to support the 1981 student protests campaigning for Kosovan independence in Pristina, Kosovo.

Thunder surprised everyone in their return to the top flight, clinching the 2009 Victorian Premier League Minor Premiership with a lead of 12 points.

Individual player achievements included youngster Jack Hingert being selected to play for A-League side North Queensland Fury and Joey Di Iorio winning the golden boot.

Young winger Matthew Millar was the club's top goalscorer with seven goals, also winning the NPL Rising Star award.

In 2015, Thunder slashed its budget in an attempt to reduce club debt, and replaced many higher earners with young and inexperienced but talented players.

Then manager Dean Hennessey also departed, joining Hume City, and the club brought in Stuart Munro as the new head coach.

In the off-season, Thunder named Huss Skenderovic as the coach for the 2016 NPL1 season,[6] and announced the signings of former Melbourne Victory FC player Kristian Sarkies,[7] former Socceroo Simon Colosimo and English striker Brandon Barnes.

[8] Dandenong Thunder opened its NPL2 East campaign with 15 consecutive wins, before a 3–3 draw against NPL2 West leaders Whittlesea Ranges.

[11] Dandy's second place finish meant it went to the NPL2 promotion playoff, facing North Geelong Warriors, whom they had beaten 2–0 at Elcho Park earlier in the season.

Led by Barnes, who scored 35 goals in 28 games, winning the league golden boot again, Thunder achieved promotion by taking out the NPL2 East title.

[20][21] The result sent Thunder to the promotion-relegation playoff, where they defeated FC Bulleen Lions at Melbourne Rectangular Stadium 1-0 through a Barnes goal.