The primary objective of this study was to compare the effects on muscle metabolism of two types of aerobic training, with and without a load on the lower limbs, in adults with peripheral arterial disease (PAD). A simple blind randomized clinical trial was conducted using two groups: conventional aerobic (CG) and modified aerobic with a load on the lower limbs (MG). Both groups underwent training by walking three times a week over a 12-week period. The ratings of muscle metabolism were determined after a treadmill test with constant velocity and inclination concomitant with the use of near infrared spectroscopy (NIRS). Altogether 40 individuals with PAD (CG = 65.45 ± 10.60 and MG = 63.10 ± 10.54) were included in the study. After the intervention, in both groups, there was a reduction in the relative time to recovery (p = 0.002), an improvement in the re-oxygenation rate (p = 0.017), an increased time of resistance after reaching the lowest muscle oxygen saturation (StO2) (p < 0.001), an increase in the distance walked (p < 0.001), and an improvement of the walking economy relative to StO2 (p < 0.001). After 12 weeks of training, an improvement in the deoxygenation rate was observed in both groups (p = 0.002), but with a greater magnitude in the CG (p = 0.017). Only the CG presented an increase in time to reach the lowest StO2 on the treadmill after the intervention (p = 0.010). The traditional aerobic training was superior to the modified training in relation to the improvement of muscle metabolism in patients with PAD.