This study aimed to evaluate the effect of differences in trainer skills on horse training during the early stages of riding habituation by measuring the levels of stress and changes in stress levels. Among nine untrained horses employed, five in Group A were trained by two low‐skilled trainers, whereas the remaining four in Group B were trained by two high‐skilled trainers using the traditional Kazakh method. Salivary α‐amylase concentration was measured as a biomarker of stress immediately before and after each riding session during the training period. In the duration of riding and mooring times to the total riding habituation time for each horse, no significant difference was observed between the two groups. In contrast, the mean total stress and mean final stress were significantly lower in Group B than in Group A, and the mean total change in stress before and after riding habituation was significantly higher in Group B. Differences in trainer skills were evidenced as differences in training methods to suppress the total stress levels through differences in the application of stress burden during the training of individual horses.