The study attempted to use an indicator approach to identify food, nutrition and health vulnerability in existing agriculture systems in the hilly areas in south Asia and to identify the best adaptation strategies to ensure food security. The farming system units (FSUs) were selected randomly from sites at elevation ≥ 300 m amsl, slope ≥ 30%, and representing ≥ 30% of the agrarian population. A questionnaire survey helped recognize different farming systems and their components. Adaptation strategies to reduce food-nutrition-health vulnerability (FNHV) of 424 FSUs in Sri Lanka (Hatton and Welimada), Bangladesh (Chittagong), and Nepal (Jhikhu Khola) were assessed by the FNHV index (FNHVi) calculated using 18 climate-sensitive parameters. The spatial distribution of FNHVi (0 = least to 1 = very-highly vulnerable) was mapped for each site, and a composite index compared FNHVs among sites. The FNHVi ranged from 0.13 to 0.68 and was not dependent on the altitude of FSUs. Chittagong was the most vulnerable, with a composite FNHV of 0.51, followed by Welimada (0.42), Hatton (0.39), and Jhikhu Khola (0.35). The contribution of the selected parameters to FNHV varied among different sites and households within a location. Good adaptation strategies such as crop diversification, mixed cropping, incorporation of organic fertilizers with mineral fertilizers, integrated crop and animal husbandry, and production of food for own consumption coupled with land ownership, diversified income sources, availability of storage facilities, and adoption of proper sanitary conditions have helped build climate-resilience in the mountain ecosystems of south Asia.