Literacy skills are essential if students are to access knowledge and achieve academic success in middle school science. A key difficulty with interpreting literacy practices in any discipline is the problem of conceptualising what constitutes literacy. Our study contributes new understandings to the discipline of science where there are ongoing debates concerning the meaning of literacy and confusion regarding what constitutes essential literacies in the field. Our scoping review first identifies how literacy in middle school science is conceptualised in empirical studies published between 2006 and 2019 and, second, addresses a significant gap in understandings by identifying how dominant discourses inform practice. Specifically, our findings show the dominance of a narrow conception of literacy in the science classroom relating to skills-based pedagogic instruction. Based on our review, we conclude that the field of science requires a broadening of what constitutes literacy, and engagement with New Literacy Studies which focuses on literacy as a social practice closely interwoven with student identities.