On 1 July 2011, Cowie signed for Cardiff City on a three-year contract, following newly appointed Cardiff manager Malky Mackay to Wales having been convinced not to sign an improved contract at Watford so Cardiff would not have to pay for the transfer. He made his debut for the club away at West Ham United in a shock 1–0 win on the opening day of the Championship season. Cowie scored his first and second goals for the Bluebirds in a 5–3 win over Huddersfield Town in the League Cup. He scored his first league goal of the season in a 1–1 draw with Blackpool at Bloomfield Road. Cowie scored two more goals in two goal fests which included a 4–3 loss at Peterborough United and a 5–3 victory against Barnsley at Cardiff City Stadium. He made his 400th career appearance in a 1–0 win over Crystal Palace in the League Cup, a tie which saw Cardiff reach their first-ever final in the competition. Cowie played the entirety of the Wembley final against Premier League Liverpool, but after a 2–2 draw following extra time, the Reds won the final 3–2 on penalties, a shootout in which Cowie took and converted Cardiff's second penalty.