Wagner made his collegiate debut against Fresno State on September 12, 2009, after redshirting in 2008. During his rookie season, Wagner appeared in 12 of the 13 games. Wagner got his first career start as right tackle against Arizona State on September 18, 2010. He finished the game with a loss but was credited with a victory due to an NCAA rule that if one team falls behind by seven points at any time during the fourth quarter, they can't lose that game no matter what happens from that point on. He finished his freshman year with 34 appearances and three starts. Wagner returned for his sophomore season in 2011 and started 11 of 12 games until he was sidelined for four weeks with a knee injury. He returned for the Sun Bowl where he helped lead Nebraska to its second bowl win in school history. Wagner ended his sophomore season with 70 tackles (44 solo) and 5.5 sacks. Wagner entered his junior season in 2012 as one of only two returning starters from last years squad, along with center Brett Kalina. He started all 13 games at left guard and was part of a senior-laden offensive line that paved the way for Adrian Peterson to run for 1,947 yards and 21 touchdowns. Wagner ended his third season with 79 tackles (50 solo) and 7.5 sacks.