Content and language integrated learning (CLIL) programmes are mushrooming in many different contexts. However, research has mainly focused on their impact on foreign language learning and to a lesser extent on L1 development, whereas the number of studies undertaken in multilingual contexts in which more than two languages coexist is negligible. In an attempt to fill this gap, the overall aim of this research study was to examine the effect of CLIL on the learning of three languages in contact, namely English, Basque and Spanish in the Basque Country, Spain. With this objective in mind, two test rounds were conducted in a longitudinal study spanning one year and in which 285 secondary education students took part. The results revealed significantly higher scores on the part of the CLIL students in English (which represents the L3 and the foreign language in this context) in both test rounds, although a similar linguistic development between the experimental CLIL and the control non-CLIL groups was observed. Additionally, no significant differences were found in the students’ L1 and L2 development (Spanish and Basque), despite the fact that CLIL students had a lower exposure to Basque in the school context.