Gastrocnemius weakness is associated with Achilles tendinopathies and muscle strains, with the medial gastrocnemius (MG) more commonly injured than the lateral gastrocnemius (LG). Walking and jogging are common in daily activities and sports, and biomechanical differences between shod and barefoot exercise may influence MG and LG activation. Understanding these activation patterns could help optimize training programs for injury prevention and/or rehabilitation. The aim was to compare MG and LG electromyographic activity during walking and jogging, both shod and barefoot. Twenty-nine participants (25.28 ± 4.53 years, 171.31 ± 0.76 cm, 72.68 ± 6.36 kg) completed a warm-up followed by 1 min of walking (80–99 steps/min) and jogging (130–150 steps/min) in both conditions (barefoot and shod, random order). Electromyographic signals were recorded using wearable devices (mDurance Solutions S.L., Granada, Spain; 1024 Hz sampling rate). We measured the root-mean-square (RMS) amplitudes for an entire stride cycle and digitally filtered the signals. For analysis, we normalized electromyographic values to the average peak values obtained during two sprints. We analyzed differences with a repeated-measures analysis of variance. Significant effects of condition (barefoot-shod) and gastrocnemius (MG-LG) were observed (all p ≤ 0.023, ƞp2 = 0.17–0.39), with higher MG activation compared to LG in the barefoot conditions (p = 0.004–0.027, d = 0.72–0.83), and nonsignificant differences between muscles in the shod conditions (p > 0.05). Shod exercise compared to barefoot resulted in lower MG activation (p = 0.001–0.003, d = 0.62–0.63) and non-significant differences in LG activation. These results indicate that barefoot walking and jogging increase MG activation compared to shod conditions, with no differences in LG activation. Additionally, footwear reduces differences between MG and LG.