The following year, Port were minor premiers in the VPL for the first time in their history, but successive losses in the finals series meant the season finished on a disappointing note.

Port Melbourne made an application to join the NSL ahead of the 1995/96 season[2] however this move was not approved and the club remained in the Victorian system.

After spending two-years in State 2 South East, the FFV unilaterally decided to place them in Division 2 North West in Season 2010.

In their first season back in the Victorian top-flight, the Sharks would have qualified for the finals had the league not been compromised by the Southern Stars FC scandal[5][6] and the club ended 2013 with a 6th-place finish.

In 2014, the first year of the National Premier Leagues system, Port Melbourne were seconds away from relegation until a 95th-minute goal from Conor Reddan in the final game of the season secured a draw against Werribee City, safety for the club and an 11th-place finish.

[9] In 2016, Port Melbourne were dealt three blows early on in the transfer window, with Kamal Ibrahim[10] and Nicholas Krousoratis[11] left for NPL rivals, but the club replaced them with the signings of Bonel Obradovic from Northcote City, David Stirton from South Melbourne[12] and welcomed back former player Lambros Honos, who rejoined the club he spent 2013 and 2014 with, after spending a season at Oakleigh Cannons.

[16] Following an 11th-place finish in 2017, the club parted ways with Barba[17] and appointed Adam Piddick who previously coached in the National Premier Leagues Queensland.