As climate change continues to exert increasing pressure upon the livelihoods and agricultural sector of many developing and developed nations, a need exists to understand and prioritise at the sub national scale which areas and communities are most vulnerable. The purpose of this study is to develop a robust, rigorous and replicable methodology that is flexible to data limitations and spatially prioritizes the vulnerability of agriculture and rural livelihoods to climate change. We have applied the methodology in Vietnam, Uganda and Nicaragua, three contrasting developing countries that are particularly threatened by climate change. We conceptualize vulnerability to climate change following the widely adopted combination of sensitivity, exposure and adaptive capacity. We used Ecocrop and Maxent ecological models under a high emission climate scenario to assess the sensitivity of the main food security and cash crops to climate change. Using a participatory approach, we identified exposure to natural hazards and the main indicators of adaptive capacity, which were modelled and analysed using geographic information systems. We finally combined the components of vulnerability using equal-weighting to produce a crop specific vulnerability index and a final accumulative score. We have mapped the hotspots of climate change vulnerability and identified the underlying driving indicators. For example, in Vietnam we found the Mekong delta to be one of the vulnerable regions due to a decline in the climatic suitability of rice and maize, combined with high exposure to flooding, sea level rise and drought. However, the region is marked by a relatively high adaptive capacity due to developed infrastructure and comparatively high levels of education. The approach and information derived from the study informs public climate change policies and actions, as vulnerability assessments are the bases of any National Adaptation Plans (NAP), National Determined Contributions (NDC) and for accessing climate finance.