Milligan, 28, has arguably become the team's most important player since arriving in 2012, initially on loan from JEF Chiba United.
Able to play in central midfield and defence, the versatile former Sydney FC man has been linked with moves away to the Middle East and Europe in the last year.
Crystal Palace were close to securing his services following their promotion to the Premier League at the beginning of last season.
And while Victory have moved to bring in Besart Berisha and re-sign Guilherme Finkler ahead of 2014-15, supporters remained concerned Milligan could be lured away, particularly if he impresses for Australia at next month's World Cup.
However, with veteran forward Archie Thompson to be paid within the salary cap under the terms of his new contract, Victory are now set to bestow domestic marquee status upon their prized asset.
Speaking at the club's supporter forum on Monday, head coach Kevin Muscat confirmed the impending upgrade in his captain's status.
KM: Archie will fall under the cap and Mark Milligan will become our Aussie marquee #mvfcforum— Melbourne Victory (@gomvfc) May 19, 2014
Milligan is yet to agree a new contract, with his existing deal due to run out at the end of next season. Nominating the skipper as domestic marquee will enable the club to make a generous offer in negotiations, as well as make room in the salary cap for other recruitment.