Background: The methodological approach to plyometric training can influence the magnitude of adaptations by accumulating acute responses that result in long-term adaptations. However, there is a lack of studies comparing cluster methods and traditional models of plyometric training organization regarding the magnitude of medium-term adaptations. Objective: This study aimed to compare cluster and traditional repetition methods on the resulting adaptations in jump performance, speed, and change of direction in young soccer players through plyometric training. Methods: A randomized controlled study was conducted over 6 weeks. In total, thirty male youth soccer players participated in the study, with nine allocated to the traditional training method group (TRD) (age = 14.83 ± 0.52 years) where they performed 3 × 10:225 s, ten players assigned to the cluster training group (CS) (age = 14.50 ± 0.52 years) where they performed 3 × 5 × 2:30s:45 s, and 11 athletes allocated to the control group (CON) (age = 14.73 ± 0.46 years). Players were evaluated pre-and post the 6 weeks of training in the 30-meter sprint (T30), change of direction (COD 505), countermovement jump (CMJ), and standing long jump (SLJ) tests. Results: Significant improvements were observed in the T30 (p < 0.001), COD 505 (p = 0.039), and CMJ (p < 0.01) for the time factor (pre vs. post) but not for SLJ (p = 0.49). Between-subject effects showed significant differences in T30 (p < 0.01) and COD 505 (p < 0.01), favoring the CON group over both training groups. The interaction between time and training method revealed significant differences for COD 505 (p < 0.01) and CMJ (p = 0.01), with the CON group showing better performance in COD 505 compared to both CS (p < 0.01) and TRD (p = 0.01) groups. No significant improvements were noted in SLJ across groups (p = 0.06). Conclusion: Plyometric training through both traditional and cluster set methods did not outperform the control condition in most measures, with the control group even showing a greater COD 505 performance compared to CS and TRD groups. Given that, regular soccer training might be sufficient for improving the assessed physical tests in young athletes, or the plyometric interventions might need adjustments in volume or intensity to yield more significant improvements.