Students studying English as a Medium of Instruction (EMI) programs, particularly in economics, often face challenges due to students’ insufficient academic literacy and content-language misalignment. The rapid rise of Generative Artificial Intelligence (AI) introduces a new dilemma; while it potentially displaces low-level linguistic tasks, it also raises worries about academic integrity and learning competence. This study evaluates academic skill deficits in preparatory courses (Pre-EMI courses) and examines students’ shifting perceptions of essential disciplinary literacies in the AI era. To achieve this aim, an explanatory sequential mixed methods design was used. To be specific, a quantitative survey (N=64) and qualitative interviews (N=5) gathered data from senior economics students on the effectiveness of preparatory courses, the necessity of 21 academic skills, and their value shift due to Generative AI. The quantitative data were analyzed descriptively, and the qualitative data were analyzed thematically to reveal a significant preparedness deficit across all skills, notably in critical evaluation of information, argument development in academic writing, and higher-order analytical skills. Importantly, although AI reduces the need for basic linguistic mechanics, the students affirm the importance of higher-order cognitive skills such as critical analysis, data interpretation, and discipline-specific reasoning. The findings confirm that success in EMI requires procedural disciplinary literacy and thus, suggest an urgent need to restructure preparation courses to integrate discipline-specific skills and critical AI literacy to close the identified skill gaps.