CLIL (Content and Language Integrated Learning) is a teaching method in which learners evolve linguistic competence and problem-solving abilities by learning content subjects in another language. However, learners’ cognitive gains may depend on their affectivity. Negative affect impedes intricate cognitive processing essential for problem-solving, while experiences of failed intellectual effort may lead to impaired information processing called intellectual helplessness (IH) (Sędek and McIntosh 1998). Negative affectivity amid children in CLIL programmes may be induced by ill-managed classes and linguistically inadequate materials (Otwinowska 2013). This paper examines links between affectivity and cognition in upper-primary Polish children (N = 140) who learn mathematics and science in English. To that end, it employs qualitative and quantitative measures to check whether negative emotions impede cognitive processes. Children completed an anonymous attitude survey and the IH Scale (Sędek 1995) to explore their affective state and symptoms of cognitive demobilization (inhibition in active problem-solving). The paper also attained children's term grades in mathematics, science and English to explore possible relationships between children's accomplishments in those subjects and their affective responses to the CLIL modules. The study discloses symptoms of IH and negative affectivity experienced by young CLIL learners. The significant predictors of IH in the CLIL classes are negative affectivity and grades in science and mathematics. Nonetheless, grades in English do not significantly forecast IH in CLIL. This paradox is explained in terms of different types of language needed in general English and CLIL classes: basic interpersonal communication skills vs. cognitive academic language proficiency (Cummins 1979).