We examined the influence of individual and contextual characteristics on student-athlete identities and then explored identity variations across the undergraduate college years. Our main analysis relied on a quantitative study of a large sample of cross-sectional data (n = 862: females = 490, males = 372) with follow-up data for 102 participants. We also used qualitative semi-structured interviews within a small sub-sample (n = 4) who participated in international competitions to provide deeper insight into their identities across time. We used the Portuguese version of the Baller Identity Measurement Scale (BIMS) to explore student-athlete identities, and we examined the influence of sex, student-athlete status (based on institution documents), the participant's competitive level in the sport, and the student athlete's university type. We modelled response probability on BIMS items with multilevel ordinal regression in a cumulative model based on the Bayesian framework. For the follow-up in-depth qualitative interviews of four participants competing at the international level, we used thematic analysis, with two independent researchers generating thematic codes. We found a non-significant trend toward a decreased student-athlete identity across the undergraduate years. Participants' statements reflected their difficulty combining both aspects of the student-athlete identity, such that they tried to shift their identities, depending on the circumstances, while their athletic identity seemed to be privileged. Hence, participants had difficulty combining a dual academic-sport career within a context oriented toward academic achievement and transition to professional life. The higher education context was unprepared to support student-athletes toward a dual academic-sport career.