Since CLIL (Content and Language Integrated Learning) implementation is context-dependent, this cross-sectional quantitative study aims at assessing the impact of parental educational background on CLIL learners' content subject learning. Statistically significant differences in Science knowledge emerged in favour of bilingually educated learners at the end of Compulsory Secondary Education. Both inter- and intra-group comparisons were conducted between the experimental (CLIL) and control (non-CLIL) cohorts in each educational stage. While non-significant inter-group differences were found in Science knowledge according to parental educational background in both educational stages, statistically significant intra-group differences by contrast emerged in favour of those CLIL and non-CLIL learners whose mothers had university education, particularly in Primary Education. Non-significant intragroup differences were also observed in favour of those non-CLIL learners whose parents attended university who performed better in Science at the end of Compulsory Secondary Education. Thus, the potentially intervening variable controlled for the study (parental educational background) exerts some differential effect on content subject knowledge in both cohorts, especially at the end of Primary Education. Results from discriminant analyses provided evidence that CLIL learners' educational achievement can also be attributed to parental educational background, particularly to the involvement and homework help provided by the highest educated mothers.