The purposes of this investigation were to: (1) assess kinetic characteristics of overload, (2) examine eccentric and concentric muscle activations and (3) explore velocity measurement as a method of intensity prescription in inertial flywheel squat training. A series of two experiments were performed: one assessing kinetic and muscle activation characteristics of flywheel squat training using three progressive inertial loads. The second experiment assessed inertial load-velocity relationships using six progressive inertial loads. Peak force, net impulse, positive–negative impulse ratio and positive–negative impulse duration ratio were each statistically significant between all three load conditions (p < 0.05). Concentric vastus lateralis muscle activation was the only significant increase between inertial loads (p < 0.05). Although not statistically significant, concentric quadricep muscle activation was increased from the lowest to highest inertia. Conversely, eccentric quadricep muscle activation was reduced from the lowest to highest inertia. In the second experiment, statistically significant regression equations were observed for average concentric velocity (R2 = 0.66) and peak concentric velocity (R2 = 0.60). In conclusion, our results indicate (1) overload is possible kinetically, (2) phase-specific muscle activation responds differently to increased inertia and (3) velocity has the potential to be used for load prescription in the inertial flywheel squat.