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Women are at a particular disadvantage by the stress that climate change poses on food systems in low- and middle-income countries (LMICs) as their adaptive capacity is hampered by unequal access to resources and services and constraints to their agency. This paper proposes a methodology to identify climate–agriculture–gender inequality hotspot LMICs and subnational areas where climate hazards converge with large concentrations of women participating in food systems and social conditions that disadvantage women. The methodology applies data reduction techniques on publicly available data to compute a hotspot index that forms the basis for ranking and mapping hotspots. Applying the methodology illustrates the hottest of 87 LMICs are located in Africa and identifies crop-specific hotspot subnational areas in four focus countries. Identifying hotspots can enable targeting populations at highest risk and render future efforts to support women’s agency for climate resilience and avert increasing gender inequalities more effective.