DPMM then decided to play in Malaysia, and joined the second-tier Malaysian Premier League as a foreign-based team in for the 2005–06 season.

They won the Singapore League Cup in their first season in Singapore, but were forced to withdraw from the league competition five games before the end of the season after FIFA suspended the Brunei Football Association for government interference in its affairs, thus barring teams from Brunei from taking part in overseas competitions.

[1] The club was then promoted to the top tier of Malaysian football, Malaysia Super League via the play-offs after a 2–1 aggregate victory over Pahang.

They then had to leave the Malaysia Super League due to the deregistration of the Brunei Football Association by the Registrar of Societies.

DPMM re-entered the S.League in the 2012 season, and became dominant after the arrival of former English Premier League manager Steve Kean in 2014.

This has affected the Bruneian-based outfit greatly, with a lesser pool of local players against Singapore's (or Japan's in the case of Albirex Niigata (S)).

[13] Towards the conclusion of the 2017 S.League in November, DPMM announced their intention on their website to possibly move to the Malaysian league, which they last appeared in 2008.

Reports by Singapore press in October 2018 revealed that DPMM have submitted an official enquiry to join Thai League 1 for the 2019 season.

[18] The club would later announce that they would be competing in the 2019 Singapore Premier League,[19] but afterwards expressed an interest to join Indonesia's Liga 1 in 2020.

[20] On 15 September 2019, DPMM were confirmed to be champions of the 2019 Singapore Premier League after their closest rivals Hougang United only managed to play a 4–4 draw with Geylang International, leaving the Bruneian club with an unassailable four-point lead at the top of the table.

[23] The team was unable to fulfill the remaining fixtures due to travel restrictions between Brunei and Singapore, resulting in the inevitable exclusion from the year's SPL season.

[27] The 'B' team which began to boast import players like Shuhei Sasahara only completed two games before the season was eventually cancelled due to the COVID-19 pandemic.

[32] DPMM began the process of returning to the Singapore Premier League after the restrictions necessitated by the pandemic eased since the year 2022.

In early July 2024, just six games into the season, the club had to replace head coach Rui Capela who left for personal reasons, and appointed Scotsman Jamie McAllister in his place.