Universities are sites of both elite knowledge production and reproduction of intersecting gendered inequalities. The US National Science Foundation (NSF) ‘Increasing the Participation and Advancement of Women in Academic Science and Engineering Careers’ (ADVANCE) programme uses universities’ role as self-reflective knowledge producers to design changes promoting gender equality. This knowledge is shaped by the institutional context of its production: NSF as a funder of scientific research; US universities as participants in highly competitive markets; managerialism as a condition of modern higher education systems; and separation of basic from applied research in the hierarchy of science. The tensions and underlying power dimensions of these contexts reveal local challenges that ADVANCE interventions navigate and the broader politics shaping what and how ADVANCE discovers. Yet, as a learning-oriented intervention, ADVANCE changes over time to create and incorporate more gendered knowledge about inequalities, to legitimize feminist understandings of organizations, and to challenge the division between fundamental and applied knowledge.