Dattoli recommended Freese to Steve Kittrell, the head coach of the Jaguars baseball team at the University of South Alabama. At South Alabama, opposing teams respected his hitting ability; scouts told their pitchers: "Don't let Freese beat us. " As a junior in 2005, Freese hit . 373, with a . 443 on-base percentage (OBP), . 525 slugging percentage (SLG), and 52 runs scored in 56 games. He was seventh in the Sun Belt Conference (SBC) in average and led the school one year after Adam Lind had done so. Freese was even better in 2006, hitting . 414 with a . 503 OBP and . 661 SLG with 73 runs and 73 RBIs in 60 games. He won the SBC batting title and led the conference in RBIs. He tied for ninth in Division I in RBIs, was 12th in average and just missed the top 10 in runs scored. He made the All-Conference team at third base and was named SBC Player of the Year. He was named an American Baseball Coaches Association All-American as the top third baseman in NCAA Division I, ahead of Evan Longoria and Pedro Alvarez, among others. Kittrell considers Freese to be the best player he coached at South Alabama, where he also coached Lind, Luis Gonzalez, and Juan Pierre.