Background: Physical exercise is known to cause significant joint changes. Thus, monitoring joint behavior of athletic horses is essential in early disorders recognition, allowing the proper management. Objectives: The aims of this study were to determine the morphological patterns, physical examination characteristics and ultrasound findings of show jumping horses in training and to establish a score-based examination model for physical and ultrasound follow-ups of metacarpophalangeal joint changes in these animals. Methods: A total of 52 metacarpophalangeal joints from 26 horses who were initially in the taming stage were evaluated, and the horses’ athletic progression was monitored. The horses were evaluated by a physical examination and by B-mode and Doppler-mode ultrasound examinations, starting at time zero (T0), which occurred concomitantly with the beginning of training, and every 3 months thereafter for a follow-up period of 18 months. Results: The standardized examination model revealed an increase in the maximum joint flexion angles and higher scores on the physical and ultrasound examinations after scoring was performed by predefined assessment tools, especially between 3 and 6 months of evaluation, which was immediately after the horses started more intense training. The lameness score and the ultrasound examination score were slightly higher at the end of the study. Conclusions The observed results were probably caused by the implementation of a training regimen and joint adaptation to physical conditioning. The joints most likely undergo a pre-osteoarthritic period due to work overload, which can manifest in a consistent or adaptive manner, as observed during this study. Thus, continuous monitoring of young athlete horses by physical and ultrasound examinations that can be scored is essential.