This article reports part of the findings of a longitudinal study on the effects of a language policy implemented in 1998 on the science learning of junior secondary students. It focuses on the effects of the instructional medium on the instructional activities in science lessons. According to students’ responses to a questionnaire, EMI (English as the medium of instruction) teachers tended to adopt a more didactic approach and use less interactive activities than CMI (Chinese as the medium of instruction) teachers. In practical work, EMI students had fewer opportunities to design investigations, but tended to follow prescribed instructions. These findings are consistent with the observations on science lessons. In comparison with CMI teachers, EMI teachers spent more time on instruction and checking answers with their students, but seldom asked questions to assess students’ understanding or higher cognitive skills. While EMI students were passive and quiet during lessons, CMI students were more active in answering or raise questions. By using short, disjointed sentences, EMI teachers often failed to communicate abstract or complex concepts accurately. To resolve these problems, EMI teachers need to master the skills to express cognitively demanding concepts through context-embedded language, and to facilitate students to acquire science knowledge while building their language skills. It is also helpful to allow more time for the transition from CMI to EMI.