In the early 1930s, Cowan became Manchester City captain, succeeding Jimmy McMullan. During his captaincy the club reached two further FA Cup Finals. The first of these was in 1933, against Everton. During the match Cowan was up against Everton captain Dixie Dean. Both players were renowned for their heading ability. Matt Busby claimed that Cowan could "head a ball as far as most of us could kick it", but Dean prevailed in the aerial battle, scoring Everton's second goal with a header. The "Daily Mail" observed that Dean's presence gave Cowan a dilemma: "He was torn between a determination not to leave Dean and a desire to help his forwards. He broke down between the two." Everton were 3–0 victors, but when Cowan received his runner's up medal from the Duke of York, he remarked that he would come back next year to win. True to Cowan's word, City returned to Wembley the following year. In the 1934 FA Cup Final, Cowan became the first and thus far only Manchester City player to represent the club in three FA Cup finals. He captained City to a 2–1 victory over Portsmouth. As team captain Cowan held primary responsibility for motivating his fellow players and match tactics. This was typical for a captain of his era, as managers of the period were chiefly administrators who had little input into coaching and tactics.