We recently reported that wearing unstable rocker shoes (Masai Barefoot Technology: MBT) may enhance recovery from marathon race-induced fatigue. However, this earlier study only utilized a questionnaire. In this study, we evaluated MBT utilizing objective physiological measures of recovery from marathon-induced muscle damages. Twenty-five university student novice runners were divided into two groups. After running a full marathon, one group wore MBT shoes (MBT group), and the control group (CON) wore ordinary shoes daily for 1 week following the race. We measured maximal isometric joint torque, muscle hardness (real time tissue elastography of the strain ratio) in the lower limb muscles before, immediately after, and 1, 3, and 8 days following the marathon. We calculated the magnitude of recovery by observing the difference in each value between the first measurement and the latter measurements. Results showed that isometric torques in knee flexion recovered at the first day after the race in the MBT group while it did not recover even at the eighth day in the CON group. Muscle hardness in the gastrocnemius and vastus lateralis showed enhanced recovery in the MBT group in comparison with the CON group. Also for muscle hardness in the tibialis anterior and biceps femoris, the timing of recovery was delayed in the CON group. In conclusion, wearing MBT shoes enhanced recovery in lower leg and thigh muscles from muscle damage induced by marathon running.