Stallings received a number of national coaching awards in 1992 and was the SEC Coach of the Year twice, in 1992 and 1994. In 2000, Stallings was awarded Distinguished Alumnus of Texas A&M University. He was awarded the Legends Award from the All Sports Association in Dallas in 2001. Stallings has also received many humanitarian awards, including the Arthritis Humanitarian Award of Alabama, National Boys Club Alumni of the Year, Dallas Father of the Year, Humanitarian Award of the Lion’s Club of Alabama, and Paris Boys Club Wall of Honor.
Stallings has been inducted into the College Football Hall of Fame, Alabama Sports Hall of Fame, Texas Sports Hall of Fame, Texas A&M Hall of Fame, Gator Bowl Hall of Fame and Cotton Bowl Hall of Fame. He also received an honorary doctoral degree from Harding University.
Gene Stallings involvement in the disability community, has also been strong. His son, John Mark was born with Trisomy 21, Down syndrome, and Gene Stallings has a school for children with disabilities named after him on the University of Alabama Campus, for which he hosts a charity golf tournament every year. The playground at the school is called the John Mark Stallings Playground.