To promote internationalization in Taiwan's higher education system, one initiative is to create international programs that accommodate both international and domestic students and that use English as the medium of instruction (EMI). Most EMI studies have focused on program results; however, the current study investigates the factors that lead students to participate in EMI programs in the first place, particularly the relationship between motivation and engagement. An instrument based on Self-Determination Theory was used to collect data about second language (L2) motivation and engagement from 276 Taiwanese college students. Data analysis using MANOVA indicated significant differences in both intrinsic motivation and English learning engagement between the students participating in EMI and non-EMI programs. Multiple regressions reveal significant predictive power of both intrinsic motivation and external regulation on English learning engagement. The results suggest gradual implementation of EMI that supports faculty and student adjustment is most effective. Inclusion of practical aspects, such as internships and service learning, into EMI programs may also enhance motivation in academic engagement.