Intrinsic motivation is the psychological construct that defines our reasons and interests to perform a set of actions. It has shown to be associated with positive outcomes across domains, especially in the academic context. Therefore, understanding and identifying peoples’ levels of intrinsic motivation can be crucial for professionals of many domains, e.g. teachers aiming to offer better support to students’ learning processes and enhance their academic outcomes. In a first attempt to tackle this issue, we propose an end-to-end approach for recognition of intrinsic motivation, using only facial expressions as input. Our results show that visual cues from students’ facial expressions are an important source of information to detect their levels of intrinsic motivation (AUC =0.570, F1=0.556). We also show how to avoid potential bias that might be present in datasets. When dividing the training samples per gender, we achieved a substantial improvement for both genders (AUC =0.739 and F1=0.852 for male students, AUC =0.721 and F1=0.723 for female students).