Whole-body electromyostimulation (WB-EMS) is an innovative training method that stimulates large areas simultaneously. In order to determine the spatial distribution of WB-EMS with respect to volume involvement and stimulation depth, we determined the extent of intramuscular edema using magnetic resonance imaging (MRI) as a marker of structural effects. Intense WB-EMS first application (20 min, bipolar, 85 Hz, 350 µs) was conducted with eight physically less trained students without previous WB-EMS experience. Transversal T2-weighted MRI was performed at baseline and 72 h post WB-EMS to identify edema at the mid-thigh and lower leg. The depth of the edema ranged from superficial to maximum depth with superficial and deeper muscle groups of the mid-thigh or lower leg area approximately affected in a similar fashion. However, the grade of edema differed between the muscle groups, which suggests that the intensity of EMS-induced muscular contraction was not identical for all muscles. WB-EMS of the muscles via surface cuff electrodes has an effect on deeper parts of the stimulated anatomy. Reviewing the spatial and volume distribution, we observed a heterogeneous pattern of edema. We attribute this finding predominately to different stimulus thresholds of the muscles and differences in the stress resistance of the muscles.