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Climate change poses a greater threat for more exposed and vulnerable countries, communities and social groups. People whose livelihood depends on the agriculture and food sector, especially in low- and middle-income countries (LMICs), face significant risk. In contexts with gendered roles in agri-food systems or where structural constraints to gender equality underlie unequal access to resources and services and constrain women’s agency, local climate hazards and stressors, such as droughts, floods, or shortened crop-growing seasons, tend to negatively affect women more than men and women’s adaptive capacities tend to be more restrained than men’s. Transformation toward just and sustainable agri-food systems in the face of climate change will not only depend on reducing but also on averting aggravated gender inequality in agri-food systems. In this paper, we developed and applied an accessible and versatile methodology to identify and map localities where climate change poses high risk especially for women in agri-food systems because of gendered exposure and vulnerability. We label these localities climate-agriculture-gender inequality hotspots. Applying our methodology to LMICs reveals that the countries at highest risk are majorly situated in Africa and Asia. Applying our methodology for agricultural activity-specific hotspot subnational areas to four focus countries, Mali, Zambia, Pakistan and Bangladesh, for instance, identifies a cluster of districts in Dhaka and Mymensingh divisions in Bangladesh as a hotspot for rice. The relevance and urgency of identifying localities where climate change hits agri-food systems hardest and is likely to negatively affect population groups or sectors that are particularly vulnerable is increasingly acknowledged in the literature and, in the spirit of leaving no one behind, in climate and development policy arenas. Hotspot maps can guide the allocation of scarce resources to most-at-risk populations. The climate-agriculture-gender inequality hotspot maps show where women involved in agri-food systems are at high climate risk while signaling that reducing this risk requires addressing the structural barriers to gender equality.