Despite the rapid growth of English medium instruction (EMI) in higher education, little research has been conducted to pinpoint the challenges faced by students. This quantitative study explored the challenges posed by the secondary-tertiary transition to first-year students with different English proficiency levels in EMI higher education institutions. In addition, we also investigated students' perception of the usefulness of supplementary and mainstream education in preparing them for those challenges. 91 participants studying at two tertiary institutions in Hong Kong completed a 52-item questionnaire. The questionnaire included items in relation to three major aspects of challenges: 'academic studies and skills', 'socialization', and 'college/university life adaptation'. It was found that students with low proficiency regarded all three aspects as significantly more challenging than the high proficiency ones in their first-year studies. However, despite the different proficiency levels, students similarly perceived mainstream education to be significantly more useful than supplementary education in preparing them for those transitional challenges. The findings together suggest that more English support is needed for low-proficiency students at the tertiary level and argue that mainstream education plays an essential role in assisting students in this secondary-tertiary transition. Implications are discussed in terms of the benefits of having a general English course as perquisite for low English proficiency students before they enroll in English for Academic Purposes courses, and the development of a variety of tasks with more emphasis on communication and collaboration at the secondary level to support them in this transition.