Like any new exercise routine, there usually is soreness when you first start training to run barefoot. This soreness happens both in the muscles and on the soles of the feet. Barefoot runners find that over time, however, the soreness goes away as their muscles strengthen and adjust to the dynamics of running with a forefoot or midfoot strike. Likewise, as the soles of the feet adjust to running barefoot, they become quite good at withstanding the various surfaces on which you run.