Bothroyd remained in the Championship, joining Cardiff City, who beat off interest from newly promoted Premier League club Hull City, on 4 August 2008 in a three-year contract for a fee of £350,000. At the start of the season Bothroyd found himself in and out of the team as manager Dave Jones attempted to find his best strike partnership and, after a number of matches, Bothroyd assumed the role of first choice strike partner to Ross McCormack. On 30 September 2008, Bothroyd scored his first goal for the club when he found the net against one of his former clubs, Coventry City during a 2–1 win. It took Bothroyd just under a month to find the net again for the club when he scored twice during a 2–2 draw at Watford. Bothroyd continued in the first team but, on 1 November, he suffered a tear of his hamstring after just 13 minutes of a 2–1 defeat against Wolverhampton Wanderers, which was expected to rule him out for between 6 and 8 weeks.