Within school contexts that are socioeconomically marginalized, complex factors often lead to languages learning being devalued in ways which adversely impact students' potential, particularly their motivation to learn an additional language (L2). This paper examines the role of Content and Language Integrated Learning (CLIL) in shaping students' L2 learning motivation within a school setting that is socioeconomically marginalized, and how it may offer a solution to this challenge. Drawing on Dörnyei's (2005) theory of the L2 Motivational Self System, this study analyzes qualitative data from a Japanese/Science CLIL course taught in one such Australian secondary school setting. Although the findings confirm previous research on CLIL's generally positive influence on student motivation, it also identifies instances of a negative impact with a certain student group. The paper concludes with the implication of CLIL-based approaches for languages provision in challenging school contexts.