Whilst gender mainstreaming (GM) implementation challenges have been widely studied, scholarly works analysing attempts to engender academic research in universities and the resistances encountered remain scarce. Drawing upon GM implementation literature and feminist institutional theory, this article explores how resistance impacts universities’ implementation of the policy and the differences in the types and forms of resistance towards distinct measures for equality in research. The data comes from in-depth analysis of university documents and 13 face-to-face interviews with gender equality agents and research managers in three Catalan universities. Catalonia constitutes an interesting case due to the limited advancement towards gender equality in academic research despite a broad policy framework and high-level commitment to the strategy. The argument developed is that resistance undermines the implementation of a decentralized, participatory and transformative GM approach, the uneven implementation of measures – those requiring significant structural change encountering greater resistance - and limited involvement of research actors. While resistances to gender balance actions manifest principally as a refusal to accept responsibility for equality actions, resistances to the incorporation of the gender perspective into research content manifest as a denial of the need for change based on a distrust towards feminist knowledge, gendered constructions of scientific excellence and notions of academic autonomy. The article contributes to debates around GM implementation as well as opposition to gender change and provides novel and nuanced insights on resistances towards GM from the area of university research.