Content and Language Integrated Learning (CLIL) has become a very popular approach in the belief that it may help to improve students’ foreign language proficiency. Although some research has been conducted, there is a dearth of longitudinal studies on students’ awareness of their language learning process in CLIL programmes. In this paper 221 CLIL students from the Basque Autonomous Community (Spain) filled out a questionnaire which analysed students’ perceptions regarding the importance of grammar and language skills, their preferences for instructional activities and their self-perceived language improvement. The results revealed that the participants attached importance to all language aspects and that they preferred group work and active participation in class in the early grades, although their enthusiasm for both aspects waned with time. Finally, the longitudinal data showed that their perceived English improvement was greater in their CLIL classes than in their regular English as a foreign language classes.