 In July 2013, Stewart was appointed assistant to Coyle at Wigan Athletic who had just been relegated to the Championship.On 5 December the same year he left the club, a few days after Coyle had departed.On 31 December 2014 Stewart became assistant to Coyle at Houston Dynamo in Major League Soccer; however they were unable to steer the team to the Playoffs in the 2015 season, and in May 2016, midway through the following campaign, their 17-month stint came to an end.