Boyd made his debut for Peterborough in a 3–1 defeat away at Darlington in January 2007, and scored his first goal for the club a month later in a 3–0 win against Wrexham. He came off the bench to score Peterborough's equaliser in a 1–1 draw at home to Boston United, scoring a "superb 35-yard volley". He netted once more in a 2–0 win against Notts County, as well as creating Peterborough's second for Craig Morgan. Boyd scored his fourth goal of the season, scoring from just inside the area to give the lead away at Grimsby Town in March 2007. He scored six times for the club during the second half of the 2006–07 season, playing 20 matches – including two goals on the final day of the season in a 3–3 draw with Rochdale. The following year, Boyd was instrumental in helping Peterborough to promotion to League One, scoring 15 times in 53 matches. During the season, he scored his second professional hat–trick in an 8–2 win against Accrington Stanley. As a result, he was named in the League Two 2008 PFA Team of the Year.