Students in secondary education inevitably favour some subjects more than other subjects. This appraisal may affect how motivation relates to performance in these subjects. Whereas autonomous motivation is generally linked to positive school outcomes, the effect of controlled motivation is less clear. This study specifically focused on the associations of controlled motivation with performance in the context of favoured and disfavoured subjects. In the present study, secondary school students (N = 918) identified 2 favoured and 2 disfavoured subjects. Hierarchical linear modelling was performed to investigate the relationship of autonomous and controlled motivation with performance in these subjects. Results showed that autonomous motivation positively related to performance in both types of subjects. The association of controlled motivation with performance was negative in both contexts, and more negative in disfavoured subjects. For teaching practice, this means that teachers should always stimulate autonomous motivation, even for negatively appraised subjects.