An imbalanced adaptation of muscle strength and tendon stiffness in response to training may increase tendon strain (i.e., the mechanical demand on the tendon) and consequently tendon injury risk. This study investigated if personalized tendon loading inducing tendon strain within the effective range for adaptation (4.5%-6.5%) can reduce musculotendinous imbalances in male adolescent handball athletes (15-16 years). At four measurement time points during a competitive season, we assessed knee extensor muscle strength and patellar tendon mechanical properties using dynamometry and ultrasonography and estimated the tendon's structural integrity with a peak spatial frequency (PSF) analysis of proximal tendon ultrasound scans. A control group (n = 13) followed their usual training routine, an intervention group (n = 13) integrated tendon exercises into their training (3x/week for ~31 weeks) with a personalized intensity corresponding to an average of ~6.2% tendon strain. We found a significant time by group interaction (p < 0.005) for knee extensor muscle strength and normalized patellar tendon stiffness with significant increases over time only in the intervention group (p < 0.001). There were no group differences or time-dependent changes in patellar tendon strain during maximum voluntary contractions or PSF. At the individual level, the intervention group demonstrated lower fluctuations of maximum patellar tendon strain during the season (p = 0.005) and a descriptively lower frequency of athletes with high-level tendon strain (≥9%). The findings suggest that the personalized tendon loading program reduced muscle-tendon imbalances in male adolescent athletes, which may provide new opportunities for tendon injury prevention.