Since the end of the 1990s, an exponential growth and massive uptake of CLIL (Content and Language Integrated Learning) in the European educational systems have been taking place. Research has mainly focused on 1) the effects of CLIL on foreign language learning as well as on attitudes and motivations towards language learning; and 2) to a lesser extent its impact on multiple language learning and content learning. Nonetheless, the number of studies that have examined students’ code-switching in this type of multilingual programmes is almost non-existent. Considering this research niche, this two-year longitudinal qualitative study investigates the effects of CLIL on students’ oral code-switching in a multilingual setting, a rural high school in Galicia (Spain). Five pairs of students were selected, each pair formed by a CLIL and a non-CLIL student. The results revealed that there was a greater decrease in the number of occurrences related to equivalence, reiteration, side-comments and intersentential code-switching among CLIL students. When compared to their non-CLIL counterparts, however, there seemed to be a tendency for CLIL students to increase their switches in two categories (monitor and alignment).