Training-induced adaptations in muscle morphology, including their magnitude and individual variation, remain relatively unknown in elite athletes. We reported changes in rowing performance and muscle morphology during the general and competitive preparation phases in elite rowers. Nineteen female rowers completed 8 weeks of general preparation, including concurrent endurance and high-load resistance training (HLRT). Seven rowers were monitored during a subsequent 16 weeks of competitive preparation, including concurrent endurance and resistance training with additional plyometric loading (APL). Vastus lateralis muscle volume, physiological cross-sectional area (PCSA), fascicle length, and pennation angle were measured using 3D ultrasonography. Rowing ergometer power output was measured as mean power in the final 4 minutes of an incremental test. Rowing ergometer power output improved during general preparation [+2 ± 2%, effect size (ES) = 0.22, P = 0.004], while fascicle length decreased (−5 ± 8%, ES = −0.47, P = 0.020). Rowing power output further improved during competitive preparation (+5 ± 3%, ES = 0.52, P = 0.010). Here, morphological adaptations were not significant, but demonstrated large ESs for fascicle length (+13 ± 19%, ES = 0.93), medium for pennation angle (−9 ± 15%, ES = −0.71), and small for muscle volume (+8 ± 13%, ES = 0.32). Importantly, rowers showed large individual differences in their training-induced muscle adaptations. In conclusion, vastus lateralis muscles of elite female athletes are highly adaptive to specific training stimuli, and adaptations largely differ between individual athletes. Therefore, coaches are encouraged to closely monitor their athletes' individual (muscle) adaptations to better evaluate the effectiveness of their training programs and finetune them to the athlete's individual needs.