This study investigated the physiological and molecular responses of Wistar Hannover rats, submitted to three 5-week chronic training models, with similar training loads. Twenty-four Wistar Hanover rats were randomly divided into four groups: control (n = 6), low-intensity training (Z1; n = 6), moderate-intensity training (Z2; n = 6) and high-intensity training (Z3; n = 6). The three exercise groups performed a 5-week running training three times a week, with the same prescribed workload but the intensity and the volume were different between groups. An increase in maximal speed was observed after four weeks of training for the three groups that trained, with no difference between groups. Higher rest glycogen was also observed in the soleus muscle after training for the exercise groups compared to the control group. We also found that the Z2 group had a higher protein content of total and phosphorylated GSK3-β compared to the control group after five weeks of training. In conclusion, the present study shows that five weeks of treadmill training based on intensity zones 1, 2, and 3 improved performance and increased resting glycogen in the soleus muscle, therefore intensity modulation does not change the training program adaptation since the different program loads are equalized.