Boyd took over as the starter in 2011. Boyd led the Tigers to a 10-4 record, winning the ACC Championship and setting up a game against West Virginia in the Orange Bowl. Although the Tigers lost the Orange Bowl in record fashion, 70-33, Boyd had a highly successful year. He finished the year completing 298 of 499 passes for 3,828 yards and 33 passing touchdowns. He also ran for 218 yards and five touchdowns. He was also mentioned as a possible 2012 Heisman Trophy candidate.
During his second year as a starter in 2012, Boyd helped lead the Tigers to a 11-2 record, completing 287 of 427 passes for 3,896 yards, 36 touchdowns and 13 interceptions. On November 17, 2012 in a game against NC State State, he broke the ACC record for most touchdowns in a game. Boyd threw five touchdown passes and ran for three more, collecting eight total touchdowns and racking up 529 all-purpose yards. After the season he was named the ACC Player of the Year. In the 2012 Chick-fil-A Bowl game against the LSU Tigers, Boyd completed 36 of 50 pass attempts for 346 yards and two passing touchdowns as well as a rushing touchdown and was named the game's MVP. Following their 2012 campaign, Boyd graded both the Tigers' overall performance and his individual performance, at a 'B'.
As a senior in 2013, the Tigers went 11-2, with Boyd completing 283 of 413 passes for 3,851 yards, 34 touchdowns and 11 interceptions. On November 14, 2013 Boyd set the ACC career passing touchdowns record. In his final college game against the Ohio State Buckeyes in the 2014 Orange Bowl, Boyd helped lead the Tigers to a 40-35 victory, completing 31 of 40 passes for 378 yards and five passing touchdowns. He also had 127 rushing yards and a touhdown. His performance set an Orange Bowl record for total yards in a game.
Boyd finished his career with school records for passing yards with 11,904 and passing touchdowns with 107.