In January 2012, Stewart was confirmed as Balestier Khalsa's head coach for the season 2012 S.League campaign.
His time at Balestier were successful, as he guided the club to win the 2013 Singapore League Cup and 6th and 4th placings in the 2012 and 2013 league seasons respectively, the best positions by the club since merging from Balestier Central and Clementi Khalsa.
[5] Initially Stewart were successful, with 5-game unbeaten streak in the league and interest from hometown club Newcastle United Jets to be their head coach, which Stewart turns down to stay with the Singapore club.
[6][7] But after a string of poor results, culminating in a 7–1 thrashing at the hands of Albirex Niigata (S) in June, Stewart resigned from his position at the club.
[8] In July 2016, Stewart was appointed head coach of the Maldives national team.