Despite an abundance of research on English medium instruction (EMI) in general, few studies have concentrated on how EMI is used to teach humanities subjects. Even fewer studies have monitored the development of, and hinderances to, disciplinary literacy in a moment-to-moment fashion in EMI lectures. To address this gap, the present study investigated student comprehension challenges in an EMI philosophy of science lecture, a discipline that values argumentation and dialogue in knowledge construction. The lecturer was interviewed about her perspectives on teaching philosophy in EMI, where she emphasized the language-heavy nature of the subject. Three students used a novel footpedal device to indicate points in the lecture that they struggled to understand. The device provided “time stamps” that were used to locate the challenging episodes in the lecture video recording. Students then joined stimulated recall interviews where they described the causes of their comprehension difficulties, and thus, impediments to disciplinary learning. Findings showed students experiencing top-down challenges related to the subject-specific content the most, followed by bottom-up, environmental, multimodal, and affective aspects. Pedagogic strategies based on the findings are then provided.