Background Minimalist shoes have gained popularity recently because it is speculated to strengthen the foot muscles and foot arches, which may help to resist injuries. However, previous studies provided limited evidence supporting the link between changes in muscle size and footwear transition. Therefore, this study sought to examine the effects of minimalist shoes on the intrinsic and extrinsic foot muscle volume in habitual shod runners. The relationship between participants' compliance with the minimalist shoes and changes in muscle õvolume was also evaluated. Methods Twenty habitual shod runners underwent a 6-month self-monitoring training program designed for minimalist shoe transition. Another 18 characteristics-matched shod runners were also introduced with the same program but they maintained running practice with standard shoes. Runners were monitored using an online surveillance platform during the program. We measured overall intrinsic and extrinsic foot muscle volume before and after the program using MRI scans. Findings Runners in the experimental group exhibited significantly larger leg (P = 0.01, Cohen's d = 0.62) and foot (P