The purpose of this study was to investigate the effects of a resistance training program on the muscular strength of soccer players' knees that initially presented unilateral and bilateral differences. For this study, a team of 24 male well-trained junior soccer players was divided into two strength program training groups: a Resistance Training Control Group (RTCG) composed of 10 players that did not have muscular imbalances and a Resistance Training Experimental Group (RTEG) composed of 14 players that had muscular imbalances. All players followed a resistance training program for six weeks, two times per week, during the transition period. The program of individualized strength training consisted of two parts. The first part, which was identical in terms of the choice of training loads, was intended for both training groups and contained two series of exercises including upper and lower body exercises. The second part of the program was intended only for RTEG and consisted of two additional series for the groups of muscles that had identified unilateral and bilateral differences. The applied program showed various directions in the isokinetic profile of changes. In the case of RTCG, the adaptations related mainly to the quadriceps muscle (the peak torque (PT) change for the dominant leg was statistically significant (p < 0.05)). There were statistically significant changes in RTEG (p < 0.05) related to PT for the hamstrings in both legs, which in turn resulted in an increase in the conventional hamstring/quadriceps ratio (H/Q). It is interesting that the statistically significant (p < 0.05) changes were noted only for the dominant leg. No statistically significant changes in bilateral differences (BD) were noted in either group. These results indicate that individualized resistance training programs could provide additional benefits to traditional strength training protocols to improve muscular imbalances in post-adolescent soccer players.