Tropical ecosystems are among the most vulnerable to climate change. Understanding climate impacts on these ecosystems is a primary challenge for policy makers, ecologists, and conservationists today. We analyzed the vulnerability of ecosystems in a very heterogeneous tropical region in southern Ecuador, selected because of its exceptional biodiversity and its ecosystem services provided to people of southern Ecuador and northern Peru. The vulnerability assessment focused on three components: exposure, sensitivity, and adaptive capacity. For the first two components, we identified stressors or drivers of change that negatively influence ecosystems. For the third component, we identified existing and potential buffers that reduce impacts. This process was developed in workshops and by expert elicitation. Representative Concentration Pathway (RCP) scenarios were used, considering RCP 2.6 and RCP 8.5 for a time horizon to 2050. Under the RCP 2.6 scenario, the components of overall vulnerability in the southern region of Ecuador showed very low to moderate vulnerability for most areas, particularly in semi-deciduous forest ecosystems, Amazon semi-deciduous forest, Amazon rainforest, and mangrove forests. These areas had high vulnerability under the RCP 8.5 scenario. A variety of conservation strategies (e.g., protected areas) were shown to increase the adaptive capacity of ecosystems and reduce their vulnerability. We therefore recommend improving these conservation initiatives in ecosystems like dry forests, where the greatest vulnerability is evident.