Research evaluating the effects of running footwear on gait has deduced foot motion from upper and sole movement of footwear. The aim of the present study was to evaluate a technique that allows for direct assessment of the medial longitudinal arch (MLA) in running. A secondary purpose was to evaluate the effect of increased bending stiffness of footwear on the MLA during running. Using a unique marker set, a multi-segment foot model was created to analyze dorsiflexion of the first metatarsal, navicular displacement, rearfoot motion, and tibial rotation. Virtual markers were created based on the movement of these foot segments. Two different pairs of running shoes (flexible, stiff) were evaluated. 13 participants ran barefoot, and in both shoe conditions. The mean difference between actual and virtual markers created was 0.69 mm. Independent t-tests determined first metatarsal dorsiflexion was restricted in the stiff condition compared to the flexible (p < 0.05) with an effect size of 0.36. The study provides a useful method of assessing foot motion while wearing footwear, and indicates that stiffer shoes restrict foot motion.