Climate change poses a growing risk to global biodiversity. To prioritize conservation efforts, identification of the species and ecosystems most at risk from further changes in climatic conditions is critically needed. Although frameworks are available to assess species vulnerability to climate change, we still lack an easily implementable, ecosystem-level perspective to inform landscape management. Here, we introduce a novel, spatially explicit vulnerability framework able to generate assessments at the ecosystem scale and apply it to Mozambican forest mangroves, which are under growing pressures from climate change. Results show that most of these ecosystems are currently highly vulnerable to sea level rise, while mangroves in the Zambezia and Nampula districts are highly vulnerable to both sea level rise and tropical storms. Altogether, we believe the introduced assessment framework has clear potential to inform conservation planning and management at various spatial scales, and help achieve adaptive management in the face of climatic uncertainties.