As a sophomore in 2006–07, Zeller started the first 16 games of the season and played in all 32 contests, while averaging 3.8 points and 2.2 rebounds per game. On December 16, 2006, he scored a then career-high 14 points in a 94–63 win over Elon. On March 9, 2007, he scored four points in 18 minutes in the team's Big East Championship semi-final loss to Georgetown. At the season's end, he was named the recipient of the Notre Dame Club of St. Joseph Valley Rockne Student-Athlete Award. In August 2007, Zeller travelled with Athletes in Action to Australia where he played in eight exhibition games and averaged 11.3 points and 6.6 rebounds while netting double figures in five of those contests. As a junior in 2007–08, Zeller earned the Notre Dame Most Improved Player Award after averaging 4.5 points and 2.2 rebounds coming off the bench in all 33 contests. As a senior in 2008–09, Zeller served as one of four captains. He played in all 36 games and earned seven starts during his final season, averaging a career-high 4.9 points per game, while bringing down 2.8 rebounds per contest. Zeller had a career outing against USC Upstate in the season opener as he came off the bench in 19 minutes of action to score a career-high 18 points on 6-of-7 from the field and was 4-of-6 from three-point range. In addition to the 18 points, he grabbed five rebounds. On November 24, 2008, he recorded his first career double-double in win over Indiana at the EA Sports Maui Invitational as he finished with 10 points and a career-high 11 rebounds. He concluded his career tied for third with 128 games played; he made 32 career starts and averaged 4.2 points and 2.5 rebounds per game. College statistics |- | style="text-align:left;"| 2005–06 | style="text-align:left;"| Notre Dame | 27 || 9 || 13.7 || .364 || .339 || .471 || 3.1 || 1.0 || .1 || .3 || 3.4 |- | style="text-align:left;"| 2006–07 | style="text-align:left;"| Notre Dame | 32 || 16 || 12.4 || .489 || .395 || .667 || 2.2 || .5 || .3 || .4 || 3.8 |- | style="text-align:left;"| 2007–08 | style="text-align:left;"| Notre Dame | 33 || 0 || 11.8 || .426 || .381 || .538 || 2.2 || .4 || .4 || .2 || 4.5 |- | style="text-align:left;"| 2008–09 | style="text-align:left;"| Notre Dame | 36 ||