The purpose of this study was to compare the muscle activation of the scapula, leg, and trunk between the front squat (FS) and overhead squat (OHS). Seven recreationally trained men (age: 28 ± 3.6 years, body mass: 92 ± 26.1 kg, height: 175 ± 5.3 cm, 3-RM front squat test: 125 ± 49.8 kg, 3-RM overhead squat test: 91 ± 15.5 kg) participated in this within-subject crossover design. Two isometric exercises (plank and Biering-Sorenson back extension) were also included for trunk musculature comparisons. Electromyographic activity of the vastus lateralis (VL), biceps femoris (BF), thoracic region of erector spinae (ES), middle trapezius (MT), rectus abdominis (RA), external oblique (EO), serratus anterior (SA), and anterior deltoid (AD). Differences in EMG during the FS and OHS were analyzed using a 2 × 3 (squat variation X intensity) repeated measures analysis of variance (ANOVA), effects were further analyzed by paired t-tests. Results showed that SA and AD activity was significantly greater (p < .05) during both concentric and eccentric phases of the FS. RA and MT activity was significantly greater (p < .05) during both concentric and eccentric phases of the OHS, and EO activity was significantly greater (p <.05) during the eccentric phase of the OHS. The FS and OHS showed greater (p < .05) ES activity when compared to the Biering-Sorenson back extension and the trunk muscles (RA, EO) during the plank was significantly greater (p < .05) than the FS, but not the OHS (p > .05). Results of the study show that on top of strengthening lower body and abdominal musculature, the FS and OHS can help strengthen muscles supporting the shoulder complex and scapula.