Objectives This study investigated if gradually introducing runners to minimalist shoes during training improved running economy and time-trial performance compared to training in conventional shoes. Changes in stride rate, stride length, footfall pattern and ankle plantar-flexor strength were also investigated. Design Randomised parallel intervention trial. Methods 61 trained runners gradually increased the amount of running performed in either minimalist (n = 31) or conventional (n = 30) shoes during a six-week standardised training program. 5-km time-trial performance, running economy, ankle plantar-flexor strength, footfall pattern, stride rate and length were assessed in the allocated shoes at baseline and after training. Footfall pattern was determined from the time differential between rearfoot and forefoot (TDR–F) pressure sensors. Results The minimalist shoe group improved time-trial performance (effect size (ES): 0.24; 95% confidence interval (CI): 0.01, 0.48; p = 0.046) and running economy (ES 0.48; 95%CI: 0.22, 0.74; p < 0.001) more than the conventional shoe group. There were no minimalist shoe training effects on ankle plantar-flexor concentric (ES: 0.11; 95%CI: −0.18, 0.41; p = 0.45), isometric (ES: 0.23; 95%CI: −0.17, 0.64; p = 0.25), or eccentric strength (ES: 0.24; 95%CI: −0.17, 0.65; p = 0.24). Minimalist shoes caused large reductions in TDR–F (ES: 1.03; 95%CI: 0.65, 1.40; p < 0.001) but only two runners changed to a forefoot footfall. Minimalist shoes had no effect on stride rate (ES: 0.04; 95%CI: −0.08, 0.16; p = 0.53) or length (ES: 0.06; 95%CI: −0.06, 0.18; p = 0.35). Conclusions Gradually introducing minimalist shoes over a six-week training block is an effective method for improving running economy and performance in trained runners.