The purpose of this study was to compare the effects of a standard flexible shoe and a stability running shoe on lower limb muscle activity during walking. Twenty-eight young asymptomatic adults with flat-arched feet were recruited. While walking, electromyographic (EMG) activity was recorded from tibialis posterior and peroneus longus via intramuscular electrodes; and from tibialis anterior and medial gastrocnemius via surface electrodes. Three experimental conditions were assessed: (i) barefoot, (ii) a standard flexible shoe, (iii) a stability running shoe. Results showed significant differences for the peak amplitude and the time of peak amplitude for tibialis anterior, peroneus longus and medial gastrocnemius when comparing the three experimental conditions (p < 0.05). Significant differences were detected primarily between the barefoot and shoe conditions and with relatively small effect sizes for peroneus longus, tibialis anterior and medial gastrocnemius. Few significant differences were found between the two shoe styles. We discuss how these changes are most likely associated with the shoe upper bracing the foot, the shape of the shoe outer-sole and weight of the shoes. Further research is needed to investigate differences between these shoe styles when participants walk for longer distances (i.e. over 1000 m) and following fatigue.