In Hong Kong, transfer students encounter different challenges unfolding in their transition from community college to university study. However, limited research has been conducted to explore their discipline-specific challenges. To address this gap, in this study three engineering and science faculties were selected from which to collect data through 35 in-depth interviews with transfer students, followed by a thorough thematic analysis. With the concept of in-betweenness, three main themes were identified: (1) “shifted the focus of study” (three sub-themes: (i) academic excellence in community college; (ii) future career in the university; and (iii) university life); (2) “encountered challenges in the transition” (four sub-themes: (i) non-matching program articulation; (ii) heavy study workload and its associated consequences; and (iii) non-specific administration arrangement and support from university); and (3) “students’ voices to enhance learning experiences” (four sub-themes: (i) modify the study duration; (ii) improve program articulation; (iii) improve social adjustment; and (iv) overseas exchange). The results of this study indicate the challenges faced by transfer students in their transition from community college to university and have implications for universities to design and implement appropriate strategies to prepare for the future.