Jones began coaching basketball in 1986, when he returned to his alma mater to direct the Detroit Southwestern basketball program. He served as an assistant for the varsity team and the head coach for the junior varsity team. At Southwestern, Jones had experience working with the likes of
Jalen Rose,
Howard Eisley, and
Voshon Lenard. He led them to a
USA Today mythical national championship in 1991. Later on, he began coaching Team
AAU Michigan, a post that he would hold until 1993, when he secured an assistant coaching position at the
University at Buffalo. Jones moved on to
Toledo University in 1996 and then the
University of Wisconsin–Milwaukee in 2001. At Milwaukee, he coached his first games with
Bruce Pearl, who he would stick with when he coached at the
University of Tennessee and
Auburn University, whom he would join in 2005 and 2014 respectively. On July 14, 2015, Jones assumed his position as interim head coach with the Express following the suspension of original coach, his brother
Bill Jones, in the midst of the
2015 NBL Canada Finals brawl. Tony said, "[Bill and I] haven't been together for a year in over 25 years. Either I was coaching collegiately, he was playing professionally at different levels, or he was coaching." Jones coached the Express for 20 games and a 10–10 record until his brother's suspension was lifted. Jones remained as assistant coach for the rest of the season. Jones was hired as assistant coach for the
Oakland Golden Grizzlies men's basketball team for the
2017–18 season. He replaced assistant Cornell Mann who left the program to become assistant coach at
Missouri. ==Personal==