This article reports on an intervention study of reading comprehension among young learners of English as a third language (L3) in a multilingual (Spanish-Basque-English) context in the Basque Country. The study involves a pre-test post-test design, with an intervention of 7 weeks using two intact groups of participants that served as experimental and control groups in CLIL classrooms, where a number of subjects are taught through the L3: English. Findings indicate that reading awareness and strategy use were enhanced following the training. While both the control and the experimental group improved over time, the experimental group showed statistically significant gains in reading comprehension, outperforming the control group. Furthermore, this difference was maintained over a two-year period, with the experimental group showing a marked improvement in reading competence. This study has implications for the fields of learning strategies and instructional strategies with respect to children learning a foreign language in CLIL contexts.