The few studies conducted to date on the affective dimension of CLIL (Content and Language Integrated Learning) have predominantly focused on the relationship between motivation and language attainment, which points to a need for further investigation. To this end, this cross-sectional study aims at researching the degree of correlation between motivational variables and content learning achievement. With that goal in mind, discriminant and correlation analyses were performed with the motivational variables scrutinised (willingness and self-esteem, self-demand, anxiety and lack of interest) to determine to what extent such motivational variables may influence and account for the variance of student performance results in the subject of natural science obtained by the experimental (CLIL) and control (non-CLIL) groups at the end of primary and secondary Education. Contrary to expectations and the reviewed literature, the findings of the study revealed a low correlation between the motivational variables scrutinised in the study and content learning achievement in CLIL programmes. It was also found that not all motivational variables exert the same effect on the CLIL learners' content achievement which may be affected, to some extent, by the influence of both self-demand and lack of interest.