The neoliberal reorganization of higher education has reshaped the research and education missions of university science. Much of the scholarship examining this shift focuses on faculty experiences. This dissertation centers the experiences of student scientists to explore: (1) how entrepreneurial universities manage marginal academic knowledge workers, including students, through processes that shift responsibility onto individual workers; (2) how universities use mechanisms like internships and Individual Development Plans to shift educational responsibilities onto students; and (3) how performances of masculinity in commercial spaces of university science contribute to durable gender inequalities among students under academic capitalism. Longitudinal qualitative methods were employed to understand how students experience years of training in an academic capitalist context. The data for the dissertation were collected during a five-year ethnography in two academic science sites, and include 60 interviews with academic faculty, staff, and student scientists. Findings show how universities shift responsibilities for handling job market instabilities or the devalued aspects of education onto academic staff, postdocs, and students. Universities use accountability practices under the narrative that grad student scientists need to “take ownership” of their education. Universities create structures channeling undergraduate students into industry internships. Many material science graduate students also express a desire for industry experience, but faculty reliance on graduate student labor in academic labs deters students from holding internships. Internship dynamics at both undergraduate and graduate levels reveal how students are commodified under academic capitalism. This dissertation also finds that men students are integrated into commercial spaces of academic science while women are excluded. These processes of gender inequality exclude women from innovation teams as well as from many resources available to commercially focused scientists.