Drawing from (Dörnyei’s, The Psychology of the language learner: Individual differences in second language acquisition, 2005) L2 Motivational Self System, this case study delved into the L2 learning motivations of liberal arts and science English majors at a transnational university in China, where English Medium Instruction (EMI) is prevalent. The study aimed to uncover how the EMI educational setting, alongside disciplinary backgrounds, shapes students' motivational landscapes. Utilising a mixed-methods approach, a 4-point Likert scale questionnaire was first administered to 182 students, followed by semi-structured interviews with six purposively selected participants to ensure a representation of diverse perspectives. Quantitative data were analysed using descriptive statistics and an independent samples t-test to pinpoint motivational differences between the two groups, with Cohen’s d effect size test further elucidating the significance of these differences. Thematic analysis of qualitative data provided a deeper layer of insight, which, when cross-examined with quantitative results, revealed a nuanced understanding of motivational dynamics. Key findings highlighted that both student groups were driven by factors such as ideal L2 self, ought-to L2 self, international posture, and instrumentality. However, within the EMI context, liberal arts students exhibited heightened sensitivity to their ought-to L2 selves, language anxiety, and teacher influence compared to their science counterparts (p < 0.05, dCohen > 0.8). These distinctions underscore the EMI context's role in modulating motivational profiles, particularly accentuating certain motivational factors among liberal arts students. In light of these EMI-mediated motivational nuances, the study proposes several educational implications, including enhancing teachers’ professional development training, integrating English learning in EMI programmes with students’ aspirations, and fostering intercultural interactions to enrich students’ language and cultural experiences.