English for Academic Purposes (EAP) aims to equip multilingual students with the tools to effectively engage in disciplinary academic communication, especially writing. An ongoing challenge is how to transfer students’ knowledge of language from the EAP classroom into their current and future disciplines (Monbec, 2018) and how to empower them as independent learners and collaborators in their knowledge development. This paper reports on an EAP curriculum project in which first-year international science students in British Columbia were scaffolded to conduct independent comparative discourse analysis to develop their academic literacy abilities. We demonstrate how students not only improved their understanding of specific language features, but also were empowered with the critical knowledge and skills to become apprentice scholars and active members in the science community. The students were therefore legitimized as academic apprentices, rather than framed as deficient in language or victims of circumstance (Gallagher & Haan, 2017). We therefore present evidence of non-linguist language students successfully conducting independent discourse analysis to further their own language and learning goals.