Motivation to learn languages strongly correlates with language achievement, and the school context has a great influence on the motivation of young learners (YLs). A key rationale for the implementation of content and language integrated learning (CLIL) programs, therefore, was pupil motivation. Very few studies have measured motivation in this context, especially in primary schools. Even fewer have done so in bilingual areas, where the continuation of widespread use of the regional language often depends on its presence in the school system and where CLIL reduces this presence. To address these gaps, motivation towards the foreign language (FL), English, and the regional language, Basque, was measured in 399 YLs of English (aged 10-12 years) in Basque immersion schools. The learners were divided into a CLIL group (n = 230), with English as a foreign language (EFL) and CLIL lessons, and a non-CLIL group (n = 169), which received only EFL lessons. Results showed that the CLIL learners had a more positive attitude towards English and a slightly lower motivation towards Basque. This suggests that increasing the amount of exposure to the foreign language (FL) via CLIL lessons improves the motivation towards English but could decrease the instrumental motivation towards the regional language.