Football Scoop first reported the hire.
Lindsey joined the Kansas staff last month with new Jayhawks coach Les Miles after serving as offensive coordinator at Auburn.
Lindsey also has held coordinator posts at Kansas State and Southern Miss.
The Madison, Alabama, native returns to his home state, where he began his career as a high school coach at several top programs.
Lindsey replaces Neal Brown, who last week became the head coach at West Virginia.
Troy also interviewed Tulane offensive coordinator Will Hall, Louisiana-Lafayette defensive coordinator Ron Roberts and Ole Miss linebackers coach Jon Sumrall for the job.