The internationalisation of higher education has contributed to the increasing number of English medium instruction (EMI) implementation in a variety of global teaching contexts, including in Indonesia. One approach used to practice EMI is content and language integrated learning (CLIL). This responsive practice, however, is not without challenges. One main issue is that teachers have limited English language skills to practice EMI. The study reported here investigates lecturers’ perceptions of EMI practice in a university in Indonesia. Qualitative research methods, specifically incorporating five focus groups and five individual interviews were used to collect the data. Interview transcripts were then analysed thematically. Findings indicate that the teachers lack a clear understanding of EMI practice in a number of key areas including the selection of learning materials for and ways to conduct students’ learning assessment in EMI classrooms. Pedagogical implications include how to approach code-switching and how to incorporate ICT into EMI learning materials. Recommendations for strategies to support future EMI implementation are also outlined.