The study aimed to compare the chronic eccentric-overload training effects of unilateral (lateral lunge) vs bilateral (half-squat) using an inertial device, on hypertrophy and physical performance. Twenty-seven young team sports male players performed a 4 sets of 7 repetitions of inertial eccentric overload training, biweekly for 6 weeks, distributed in unilateral lunge group (UG: age: 22.8 ± 2.9 years; body mass: 75.3 ± 8.8 kg; height: 177.3 ± 3.7 cm) and bilateral squat group (BG: age: 22.6 ± 2.7 years; body mass: 79.5 ± 12.8 kg; height: 164.2 ± 7 cm). Lower limb muscle volume, counter movement jump (CMJ), power with both (POWER), dominant (POWERd) and no-dominant leg (POWERnd), change of direction turn of 90° with dominant (COD90d) and no-dominant leg (COD90nd) and 180° (COD180d and COD180nd), and 10m sprint time (T-10m) were measured pre and post-intervention. The UG obtained an increase of adductor major (+11.1%) and vastus medialis (+12.6%) higher than BG. The BG obtained an increase of vastus lateralis (+9.9%) and lateral gastrocnemius (+9.1%) higher than UG. Both groups improved CMJ, POWER, POWERd, POWERnd, COD90 and DEC-COD90, without changes in T-10m. The UG decrease DEC-COD90nd (-21.1%) and BG increase POWER (+38.6%) substantially more than the other group. Six-weeks of unilateral / bilateral EO training induce substantial improvements in lower limbs muscle volume and functional performance, although unilateral training seems to be more effective in improving COD90 performance.