Developing subject comprehension and critical thinking are both key goals of higher education. However, whilst the former is, on the whole, successfully cultivated in undergraduate students, the latter is not. Few empirical studies have investigated the relationship between subject comprehension and critical thinking. In the present paper we suggest that supporting the development of subject comprehension is not at odds with developing critical thinking. In fact, we argue that subject comprehension plays a key role in developing critical thinking skills. Using an experimental design, we demonstrate differing effects of an intervention on subject comprehension, subject-specific and general critical thinking, as a function of students’ academic background. We discuss the implications of our results for teaching in higher education.