BACKGROUND: Affect dynamics, or variations in emotional experiences over time, are linked to psychological health and well-being, with moderate emotional variations indicating good psychophysical health. Given the impact of emotional state on cardiac variability, our objective was to develop a quantitative method to measure affect dynamics for better understanding emotion temporal management in Anorexia Nervosa (AN). METHODS: The study proposed an experimental and methodological approach to evaluate physiological affect dynamics in clinical settings. It tested affective transitions and temporal changes using emotional images from the International Affective Picture System (IAPS), examining physiological characteristics of a patient with AN. The methodology involved calculating a heart rate variability index, e.g., RMSSD, and using it in a Discrete Time and Discrete Space Markov chain to define, quantify, and predict emotional fluctuations over time. RESULTS: The patient with Anorexia Nervosa showed a high likelihood of transitioning from positive to negative emotional states, particularly at lower arousal levels. The steady state matrix indicated a tendency to remain in highly activated pleasant states, reflecting difficulties in maintaining emotional balance. CONCLUSIONS: Employing Markov chains provided a quantitative and insightful approach for examining affect dynamics in a patient with AN. This methodology accurately measures emotional transitions and provides a clear and interpretable framework for clinicians and patients. By leveraging Markovian indexes, mental health professionals may gain a comprehensive understanding of emotional fluctuations' patterns. Moreover, graphical representations of emotional transitions may enhance the clinician-patient dialogue, facilitating a clearer emotional and physiological profile for the implementation of personalized treatment procedures.