CLIL (Content and Language Integrated Learning) programs are burgeoning in European school contexts due to the widespread belief that they help to significantly improve foreign language learning while content learning is not negatively affected. However, some of its purported benefits still need to be empirically confirmed. Thus, while this approach is widely believed to positively influence students’ affective stance, research studies are scant, and hardly any are longitudinal in nature. In an attempt to fill this gap, the present longitudinal study aims to analyze the impact of CLIL on different affective components. The participants are 304 secondary education students who were enrolled in CLIL and non-CLIL programs. Contrary to expectations and the reviewed literature, the downward motivational trend observed in non-CLIL students in previous studies was not found. The results also indicate that CLIL does not help to sustain students’ motivation over time, but motivation to learn the subject matter is maintained in CLIL classes.