In January 2009, Bowyer signed for Birmingham City on loan until the end of the 2008–09 season. He made his debut on 17 January at home to Cardiff City in the Championship, scoring an equalising goal in the fourth minute of stoppage time to make the score 1–1. Following the expiry of his contract with West Ham United, Bowyer signed a two-year contract with Birmingham in July 2009. He scored winning goals in consecutive Premier League matches, against Fulham and Wolverhampton Wanderers, to take Birmingham into a mid-table position at the end of November, and was part of the team that went on a run of 15 games unbeaten in all competitions, including a club record 12 unbeaten in the top flight, as they finished in ninth place, the club's best for more than 50 years.