Students' declining science interest in middle school is often attributed to psychological factors like shifts of motivational values, decrease in self‐efficacy, or doubts about the utility of schooling in general. This paper adds to accounts of the middle school science problem through an ethnographic, longitudinal case study of three diverse students' identity work from fourth‐ to sixth‐grade school science. Classroom observations and interviews are used as primary data sources to examine: (1) the cultural and structural aspects of the fourth‐ and sixth‐grade classrooms, including the celebrated subject positions, that enabled and constrained students' identity work as science learners; (2) the nature of students' identity work, including their positioning related to the celebrated subject positions within and across fourth‐ and sixth‐grade science; and (3) the ways race, class, and gender figured into students' identity work and positioning. In fourth‐grade, all experienced excellent science pedagogy and performed themselves as scientifically competent and engaged learners who recognized themselves and got recognized by others as scientific. By sixth‐grade, their identity work in school science became dramatically less scientific. Celebrated subject positions did not demand scientific thinking or robust engagement in scientific practices and were heavily mediated by race, class, and gender. Our results highlight three insights related to the middle school problem: (1) when students' social identity work was leveraged in service of robust science learning, their affiliation increased; (2) academic success in school science did not equate to affiliation or deep engagement with science; and (3) race, class, and gender figured into students' successes in, threats to, and identity work related to becoming scientific. We end the article by providing a framework and questions that teachers, teacher educators, and researchers might use to design and evaluate the equity of science education learning spaces. © 2014 Wiley Periodicals, Inc. J Res Sci Teach