Long got injured during the first half against the Indiana Hoosiers, and his foot was put in a protective boot. The second foot injury was expected to end his season. He appeared in the subsequent rivalry game against the Ohio State Buckeyes, and during the first play, he opposed Bobby Carpenter and Carpenter got a broken leg. After the game, Long appeared to need immediate surgery, which would have caused him to miss the 2005 Alamo Bowl. By the time of the game on December 28, though, he was ready to play. As the team prepared for 2006 spring practice, the left-handed Long was moved from right tackle to left tackle where he would be protecting the blindside of right-handed quarterbacks. Long entered the season for the 2006 Michigan Wolverines football team listed on numerous preseason conference and national teams as well as watchlists for awards such as the Outland Trophy and Lombardi Trophy. He was on the preseason Outland Trophy watch list along with Levi Brown, Joe Thomas, Justin Blalock, and Herbert Taylor. Long was considered the heart of the Michigan offense, and his teammates voted the redshirt junior to be a co-captain along with senior Woodley. Before the season started, Carr replaced offensive coordinator Terry Malone with Mike DeBord who had previously been offensive coordinator from 1997–1999. Following the 7–5 2005 season which was the worst Michigan season since 1984's 6–6-year, there was pressure on Carr to turn things around and he sought a lighter, faster and better conditioned team. During the offseason, Long reduced his weight from to to improve his agility, speed and conditioning. Under the new coordinator and with fitter athletes, the offensive scheme was shifted to concentrate on the zone blocking system. The system was similar to the one used by the Denver Broncos when they won back-to-back Super Bowls and by the Atlanta Falcons to help Warrick Dunn achieve a career-high in rushing yards while the team led the NFL in rushing yards in consecutive seasons. By mid-November, Michigan had flourished under the new system with an 11–0 record, and some of the credit for the success was attributed to Long, the team captain and offensive leader. Long was recognized as a first-team All-Big Ten selection by both the coaches and the media and was selected as the Big Ten Offensive Lineman of the Year. Long was also part of a Michigan record-setting