Extreme weather events (EWEs) including storms, heatwaves, floods, droughts, wildfires, and cold snaps present an increasing threat to protected habitats and species (PHAS) as well as ecosystem services they provide. Under ongoing climate change, the frequency, intensity, and spatial extent of such events are projected to increase, with disproportionately severe impacts on ecologically sensitive and conservation-priority areas. Despite this growing risk, existing vulnerability assessment frameworks for PHAS have primarily focused on long-term, gradual climatic shifts, largely overlooking the episodic and often catastrophic nature of EWEs. Here, we propose a structured methodological framework to assess the vulnerability of PHAS to extreme climatic events, based on the three IPCC vulnerability components including exposure, sensitivity, and adaptive capacity (ExP-SeN-AdC). The framework introduces the Extreme Event Vulnerability Index (EVI), an integrative metric designed to quantify vulnerability of PHAS to EWEs in a transparent, standardized, and scalable manner. The framework follows an eight-step process: (1) defining the assessment scope; (2) selecting ecologically meaningful indicators; (3) evaluating data availability and acquiring data; (4) constructing component indices for ExP-SeN-AdC; (5) computing the composite vulnerability metric; (6) evaluating uncertainties through validation and sensitivity analysis; (7) communicating and refining results through stakeholder engagement; and (8) formulating science-based conservation and adaptation recommendations. Finally, we demonstrate application of the proposed framework through a case study on Atlantic Salt Meadow habitats (Glauco-Puccinellietalia Maritimae) located within Dublin Bay’s Natura 2000 sites, encompassing a mosaic of Special Areas of Conservation (SACs) and Special Protected Areas (SPAs) under the EU Habitat Directive. The framework and its methodological approach lay the foundation for the vulnerability analysis and mapping, advancing adaptation planning, and guiding targeted interventions and conservation efforts, and the development of forward-looking conservation policies in the face of escalating extreme climatic threats.