The objective of this study was to compare (i) The effects of a flywheel and free-weight resistance training program; and (ii) The effects of performing lateral and frontal split squats as part of a flywheel-resistance training program on jumping performance, the 5-0-5 change of direction test time, and the one-repetition maximum (1RM) back squat in soccer players. Twenty-four male amateur soccer players participated in this study and were randomly and equally assigned to one of three different test groups: forward split-squat group (FSQ); lateral split-squat group (LSQ); and free-weight training group (TRAD). Athletes in the FSQ group performed a squat and a forward split squat on a flywheel device, while those in the LSQ group performed a squat and a lateral split squat (instead of a forward split squat) on a flywheel device. Each training lasted 4 weeks. The main finding was that all training groups, such as TRAD, FSQ, and LSQ, significantly improved broad jump length ( = 0.001; effect size [ES] = 0.36), 5-0-5 COD time with a turn on the dominant limb ( = 0.038; ES = 0.49), and 1RM back squat ( = 0.001; ES = 0.4). In turn, both flywheel-resistance training groups (FSQ and LSQ) significantly improved their counter-movement jump height ( = 0.001; ES = 0.8 and = 0.002; ES = 0.58; respectively) with no effect in the TRAD ( = 0.676; ES = 0.07) training group. Both free-weight and flywheel-resistance training lasting 4 weeks performed in-season contributed to significant improvement in 1RM back squat, broad jump performance, and 5-0-5 change of direction testing time, while flywheel-resistance training might be superior in counter-movement jump height enhancement in soccer players. Moreover, the manner in which split squats were performed was not a factor influencing the obtained results.