Bothroyd made a bright start to the 2009–10 season, scoring the second goal in the first ever league match at the Cardiff City Stadium in a 4–0 victory over Scunthorpe United. He celebrated his 50th league appearance for Cardiff City by scoring the fourth goal in a 4–0 win over Watford on 3 October 2009, and scored in the next away match against Sheffield United, which Cardiff won 4–3. Between 24 October and 7 November 2009, Bothroyd enjoyed his most prolific scoring run with Cardiff, scoring in three consecutive matches against Sheffield United, Nottingham Forest and Swansea City. With club captain Mark Hudson injured, Bothroyd took over as captain on several occasions during the second half of the season and scored a total of 13 goals in all competitions, the highest single season total of his career, as Cardiff reached the play-off final where he was forced off after 15 minutes due to injury.