Jones played for seven years in the Cubs and Athletics farm systems, including two seasons with the Triple-A Tacoma Tigers, and batted .283 with nine home runs in 899 minor league games between 1982 and 1989.

He managed the Madison Muskies, Huntsville Stars, Edmonton Trappers, Pawtucket Red Sox, Fort Wayne Wizards and Mobile BayBears.

In his first season with Lehigh Valley, he led the 2018 IronPigs to an 84–56 win–loss record and the International League North Division championship, although his team was eliminated in the opening round of the Governors' Cup playoffs.

He was retained when Joe Maddon replaced Renteria as manager in October 2014 for the 2015 season, and was the third-base coach for the 2016 Cubs' National League and World Series championship team.

On January 27, 2022, Jones was named first base coach for the Tigers' major league team, replacing Kimera Bartee who died suddenly in late 2021.