The aim of this study was to evaluate the effects of varying flywheel inertia on velocity and power during flywheel squats. Fifteen healthy physically active males performed 6 maximal effort flywheel half-squats at each of 0.029, 0.061, 0.089, and 0.121 kg·m2, with velocity recorded via 3D motion capture and power recorded via inbuilt transducer. Peak concentric velocity (χ² = 37.9; p < 0.001), peak eccentric velocity (χ² = 24.9; p < 0.001), mean concentric velocity (F(3) = 52.7; p < 0.001), and mean eccentric velocity (χ² = 16.8; p < 0.001) all tended to decrease with increases in flywheel inertia, whereas the ratio of peak eccentric to peak concentric power (F(3) = 4.26; p = 0.010) tended to increase. Flywheel inertia had no significant effect on peak concentric or eccentric power, or the ratio of eccentric to concentric peak or mean velocities. The best fit subject-specific inertia-velocity relationships were reported for peak concentric velocity (median linear R2 = 0.95, median logarithmic R2 = 0.97). The results suggest that velocity, rather than power, should be used to prescribe and monitor flywheel squat exercise intensities, and that individualized linear relationships between inertia and peak concentric velocity can be used for this purpose.