This study was undertaken to investigate the effect of two different concepts in a training program on muscle thickness and anaerobic power in trained cyclists. Twenty-six mountain bike cyclists participated in the study and were divided into an experimental group (E), which performed polarized training, comprising sprint interval training (SIT), high-intensity interval training (HIIT), and endurance training (ET), and a control group (C), which performed HIIT and ET. The experiment was conducted over the course of 9 weeks. Laboratory tests were performed immediately before and after the conducted experiment, including an ultrasound measurement of the quadriceps femoris muscle thickness and a sprint interval testing protocol (SITP). During the SITP, the cyclists performed 4 maximal repetitions, 30 s each, with a 90-s rest period between the repetitions. SITP was performed to measure maximal and mean anaerobic power. As a result of the applied training program, the muscle thickness decreased and the mean anaerobic power increased in the experimental group. By contrast, no significant changes were observed in the control group. In conclusion, a decrease in muscle thickness with a concomitant increase in mean anaerobic power resulting from the polarized training program is beneficial in mountain bike cycling.