Stewart was appointed manager of Stockport County in 1894 and was in charge of the club when they were elected to The Football League in 1900. He remained in charge of the club until 1911 when he took over as manager of Cardiff City, making his first signing soon after by bringing one of his former Stockport players in Billy Hardy to the club, who would go on to be a lynchpin of the side during the clubs success under Stewart. Due to the financial plight of the club at the time, Stewart paid Hardy's £25 transfer fee with his own money.
In his second year that he began to improve the clubs fortunes as they were promoted into the first division of the Southern Football League but it was after the end of World War I that he achieved his greatest success. Elected into the Football League in 1920, the club gained promotion to division one, finishing second on goal difference to Birmingham City, and reached the semi-finals of the FA Cup in its first season.
Stewart's success in the FA Cup continued as they reached the quarter-finals in two of the following three years before reaching their first final in 1925. They went on to lose 1-0 to Sheffield United, with the only goal being scored by England international Fred Tunstall, but it would only take two years before the club returned to a final, this time in 1927. They faced Arsenal and the match was tied at 0-0 until Hughie Ferguson's shot was fumbled into the net by Dan Lewis in the 74th minute, giving Stewart the record of being the only manager ever to take the trophy out of England. Unfortunatley they were never able to reproduce their trophy winning exploits and the club steadily went downhill before being relegated to Division Two in 1929, just two years after their FA Cup final victory. The clubs slide continued and they were relegated again in 1931, this time down into Division Three South. The low point came in 1933 when a 19th place finish saw Stewart decide to step down and retire.
After his retirement he remained in Cardiff to concentrate on his businesses. He died in 1954, aged 81.