The rapid expansion of English-medium instruction (EMI) in higher education has made second language motivation an important empirical topic. Drawing on Dörnyei’s L2 Motivational Self System (L2MSS), this longitudinal multiple-case study traced the motivational trajectories of two focal Taiwanese first-year undergraduates during their first semester in an EMI program. Data were collected through monthly motivational questionnaires measuring the ideal L2 self, ought-to L2 self, current L2 self, and L2 (EMI) learning experience; this was supplemented by three rounds of semi-structured interviews conducted at the beginning, middle, and end of the semester. The mixed-methods analysis examined how these motivational components dynamically interacted over time. Results indicated that the current L2 self and EMI learning experience were mutually constitutive, forming a feedback loop that drove motivational development over time. Through this reciprocal process, ideal and ought-to L2 selves were differentially activated depending on learners’ evolving perceptions of competence and the attainability of future goals. The study highlights the dynamic, individualized nature of L2 motivation during students’ transitions into EMI education. Implications for EMI pedagogy and learner support are discussed.