Although CLIL (content and language integrated learning) programmes are now globally expanding, the number of studies that have examined their impact on both multiple language learning (students’ L1, L2 and English as a foreign language) and content learning are scarce. This study investigates the effects of a CLIL programme implemented in a rural multilingual school context in Galicia, Spain. Bearing in mind the deficiencies identified in previous CLIL research, this two-year longitudinal study secured the homogeneity of the CLIL and non-CLIL samples (n = 44) before the actual implementation of the CLIL approach. Although both groups improved their competence in English after two years, the CLIL cohort made significantly greater progress. Interestingly, the CLIL students also outperformed their non-CLIL counterparts in both Spanish and Galician over the two school years, whereas content learning was not negatively affected. In the conclusions the importance of paying heed to the pedagogical features and the methodology employed in CLIL settings is underscored.