This study investigated the immediate and short-term effects of minimalist shoes (MS) and traditional running shoes (TRS) on vertical loading rates, foot strike pattern and lower limb kinematics in a group of habitual barefoot runners. Twelve habitual barefoot runners were randomly given a pair of MS or TRS and were asked to run with the prescribed shoes for 1 month. Outcome variables were obtained before, immediate after and 1 month after shoe prescription. Average and instantaneous vertical loading rates at the 1-month follow-up were significantly higher than that at the pre-shod session (P < 0.034, η2p > 0.474). Foot strike angle in the TRS group was significantly lower than that in the MS group (P = 0.045, η2p = 0.585). However, there was no significant time nor shoe effect on overstride, knee and ankle excursion (P > 0.061). Habitual barefoot runners appeared to land with a greater impact during shod running and they tended to have a more rearfoot strike pattern while wearing TRS. Lower limb kinematics were comparable before and after shoe prescription. Longer period of follow-up is suggested to further investigate the footwear effect on the running biomechanics in habitual barefoot runners.