For non-native students majoring in English-Medium Instruction (EMI) departments, it is essential to have academic language proficiency, particularly academic writing proficiency, to successfully manage their studies. In Turkey, English-medium universities offer one-year preuniversity English for Academic Purposes (EAP) programs to the students to prepare them for their English-medium studies. While there has been a growing interest in the of the EMI students' academic writing needs in recent years, far less attention has been paid to the students' developing perception of L2 writing prior to their EMI studies. Therefore, this longitudinal case study, framed within the Academic Literacies Approach, aims to investigate the changes in the prospective EMI students' perception of writing over their one-year study at the preparatory EAP writing program. The data were obtained from writing background questionnaire and students' written narratives. As a result of the qualitative analysis, the findings demonstrate that the skill-based EAP writing pedagogy, framed by the limited writing background of the students, fails to help the students develop a sense of academic literacy that can facilitate their future EMI studies. The study offers some implications for improving EAP writing pedagogy in EMI university settings to help students succeed as academic writers.