English as a medium of instruction (EMI) is commonly adopted as a strategy for higher education internationalisation. While there are numerous studies on the teaching practices of EMI programmes, the relationship between EMI and structural inequalities has been less investigated, especially in “universal” higher education systems. To address the research gap, this study investigates the EMI practices of two Taiwanese higher education institutions (HEIs) under current government initiatives. Qualitative data from policy documents and semi-structured interviews are analysed with an institutional logics approach and reflexive thematic analysis. The findings suggest that while state, managerial, and academic logics jointly shape EMI strategies in the public university case, EMI practices in the private university of technology case are predominantly driven by market and managerial logics and challenged by academic logic. Furthermore, this study reveals the structural “stuckness” encountered by the private case. In Taiwan’s hierarchical higher education system, the promotion of EMI could result in widening horizontal inequalities among HEIs. More specifically, under the EMI grading certification scheme for students and the tiered award system for HEIs, the majority may be left behind whereas the few with linguistic capital are spotlighted. Therefore, this study concludes that in light of organisational conditions, policymakers should allow greater flexibility for HEIs to develop performance indicators appropriate to their students’ needs.