Beebe has served as senior associate commissioner and chief operating officer since joining the Big 12 in 2003, following a 14-year stint as commissioner of the Ohio Valley Conference.
Kevin Weiberg is stepping down as head of the conference on July 15 to take a position with the Big Ten Network. Beebe will assume the role of interim commissioner when Weiberg departs the Big 12.
The board has also authorized the hiring of a search firm to find a new commissioner.
The Big 12 board of directors consists of the presidents and chancellors of the member institutions. Its executive committee is comprised of Harvey Perlman, chancellor at Nebraska; John Whitmore, president of Texas Tech; William Powers, president of Texas; Brady Deaton, chancellor at Missouri and Greg Geoffrey, president of Iowa State.