Cook was redshirted as a freshman in 2011. He spent the 2012 season as a backup to Andrew Maxwell. After Maxwell was benched, he helped lead the team to a win in the 2012 Buffalo Wild Wings Bowl, completing four of 11 passes for 47 yards and a touchdown. Overall, he appeared in three games, completing nine of 17 passes for 94 yards with a touchdown and an interception. He entered the 2013 season as the backup to Maxwell again. After Maxwell struggled, Cook took over as the starter after the first game and remained the starter the rest of the year.
On January 1, 2014, he led the Spartans to a 24–20 victory over the Stanford Cardinal in the 2014 Rose Bowl. He was named the offensive most valuable player.