Stewart was in charge of the side during the 1920s when the club enjoyed success by reaching two FA Cup finals, losing in 1925 before becoming the only team from outside England to win the competition in 1927.
However, the club struggled in the Football League Second Division, finishing in the bottom three in four consecutive seasons and were forced to apply for re-election on several occasions.
[5][6] Stewart took over as manager of Southern Football League Second Division side Cardiff City after responding to an advert placed in the Athletic News.
[14][16] Cardiff had become a fully professional club and joined the English football league system in 1910, finishing fourth in their first campaign under player-manager Davy McDougall.
[17] At the end of the season, the club's board decided that a full-time manager was needed to allow further progress, with Stewart the chosen candidate.
[23] In his first season, the club kept pace with the league leaders but lost form during February and finished the campaign in third place, seven points behind promoted sides Merthyr Town and Portsmouth.
[24][25] He did however lead the club to its first Welsh Cup victory by defeating Pontypridd 3–0 in a replay of the final to become the first team from the south of Wales to win the competition.
[26][27] Stewart led the side to the Second Division title, having lost only one of their 24 games with his newly formed defence proving instrumental to their success, conceding only 15 goals during the campaign.
"[22] In the First Division Cardiff initially struggled, losing their opening five matches, but Stewart was able to improve results and spent a club record £1,000 to sign Charlie Brittain from Tottenham Hotspur.
[38] During the 1923–24 season, Stewart led the side to a second-placed finish in the First Division which remains the club's highest ever league position.
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.
[29][42] Despite an increase in revenue from the final victory, the club's directors chose to spend the money on improving the facilities at their home ground Ninian Park.
[29][43] Cardiff's slide continued and they were relegated again in 1931, this time into the Third Division South as injuries and financial problems resulted in a high turnover of players.
In the 1932–33 season, Cardiff finished 19th of 22 teams in the Third Division South and Stewart chose to step down from the role after 22 years.
"[47] In his 1999 book chronicling the history of Cardiff City, journalist Grahame Lloyd wrote "He brought together men who knew their limitations to form sides who played to their strengths".
During his years with Stockport, several of his players went on to play at higher levels, the most prominent being Arthur Goddard who signed his first contract with Stewart.
[3] With Cardiff, the squad which Stewart considered the strongest of his time there, consisted of five players who had never played professionally before and had been signed from non-League sides or through youth teams: Tom Farquharson, Jimmy Nelson, Herbie Evans, Fred Keenor and Len Davies.