Gene Watson was inducted into the Texas Country Music Hall of Fame in 2002, and inducted into the inaugural class of the Houston Music Hall of Fame in August 2013. In 2018, Watson received the "Entertainer of the Year" Award from the R.O.P.E. Awards, an honor he shared with singer Jeannie Seely. It was the first time in the history of the awards that a tie occurred in any category.

Watson was invited to join the Grand Ole Opry, by Vince Gill, on January 17, 2020.