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Abstract Background Evidence shows that motivational practices focused on utility, importance, and autonomy shape university students’ motivational orientation toward learning. On the other hand, the relationship between these variables and motivational orientation toward learning is not linear and requires models that describe their behavior over time. Method In this study, mathematical modeling based on system dynamics methodology is used to simulate in health students the temporal dynamics of the motivational orientation toward learning based on the behavior of these variables in different scenarios. Results The results indicate that a) Mastery is sensitive to changes in frequency when importance and autonomy practices are performed; b) the development of Mastery is critical in the first three semesters of academic life, but its loss is hardly recoverable even when practices are incorporated in subsequent semesters; c) Utility-focused motivational practices have no significant effect on the development of learning-oriented motivation. Conclusion These findings have significant practical implications for higher education. Understanding the critical role of Mastery in the early stages of academic life and the limited potential for recovery if lost can help raise awareness of the importance of early implementation of motivational practices focused on relevance and autonomy.