In his first year at the club, the talented midfielder played in the Wizard Home Loans Cup and then followed up with a full season for the Swans Reserves, where he impressed coaching staff with his magnificent disposal skills on both sides of his body and excellent decision-making abilities in both attack and defence.

Unfortunately, Malceski ruptured his left anterior cruciate ligament during a trial game, requiring him to have a knee reconstruction, thus ruining any hopes of him making a seniors debut in 2004.

In 2005, Malceski surprised everyone by fully recovering from his knee injury both physically and mentally, and was rewarded with a seniors debut against Carlton in round eleven, the week after the Swans had suffered a 43-point loss to St Kilda which placed the entire club under severe scrutiny.

In 2007, Malceski continued to impress with exquisite disposal skills and cemented his place in the Sydney Swans team with several stand-out performances early in the season.

A great season performance in 2007 resulted Malceski to be runner-up in the clubs prestigious Skilton Medal, only second to Sydney midfielder Brett Kirk.

Malceski was part of the Sydney Swans team which won the 2012 AFL Grand Final, where he kicked his side's first and last goals of the match through miraculous snap shots.

On 6 October 2014, Malceski signed a three-year deal with the Gold Coast Football Club, parting ways with Sydney after ten seasons.