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In the present study, we explore how undergraduate students’ (N = 480) open-ended, self-generated reports of their challenges in two science courses relate to their competence, value, and cost perceptions in those courses. Challenges were coded using a bottom-up, iterative process. Multiple regression analyses revealed that students who reported experiencing challenges related to understanding course content reported lower competence beliefs, students who reported experiencing challenges with professor/course structure reported higher cost, and students who reported experiencing challenges with motivation reported lower competence beliefs, lower value, and higher cost. Linguistic analyses revealed that students who used fewer negative emotion words when describing their challenges reported higher value. These findings can inform the design of interventions that address motivational beliefs and values.