Boyd scored his first goal of the 2008–09 season in Peterborough's 2–1 loss at Bristol City. He scored again two weeks later against Hartlepool United in another 2–1 defeat, scoring Peterborough's consolation goal with a "smart finish". Boyd's third goal of the campaign came in a 1–1 draw away at Northampton Town, "finishing superbly" to give Peterborough the lead after fifteen minutes. In October 2008, Boyd netted his fourth goal of the 2008–09 season, scoring just after half-time in a 2–0 victory against Leeds United. He scored one and assisted two other goals in Peterborough's 4–0 win against Huddersfield Town, as well as providing the assist for Craig Mackail-Smith's goal against Hereford United. His sixth goal of the season came in Peterborough's 2–1 home win against Colchester United, Boyd scoring "clinically into the bottom corner from 12 yards". In the same match, he "carved open the defence on a number of occasions", and once again provided the assist for Mackail-Smith's goal. Boyd scored one and set-up another as Peterborough beat Cheltenham Town at Whaddon Road in December 2008, Boyd's goal came in the third minute of the match. A month later, he scored twice in a 4–2 win against Crewe Alexandra, and was described as "the two-goal hero" following the match – as Boyd's two goals proved to be the difference. He provided assists in matches against Yeovil Town and Hereford United respectively, and scored his last goal of the season in a 2–1 away win at Hartlepool United. Boyd ended the season by providing two assists in Peterborough's final two matches of the campaign. He scored ten times in 53 matches in all competitions, ensuring the club earned back-to-back promotions. Boyd was named in the League One PFA Team of the Year for the second successive year.