Episodic extreme coastal flooding is considered one of the most serious threats to the global coastlines, endangering infrastructure, ecosystems, and communities. The synchronized effects of extreme wave events, storm surges and astronomical tides are particularly worrying in the context of sea level rise (SLR), and a comprehensive understanding of their future dynamics remains challenging. In this study, an innovative approach for a vulnerability assessment of sandy low-lying coastal areas, based on dynamic ensemble projections is proposed. In the current Part II study, the combined effects of future projected SLR, tides, storm surges and wave action are investigated at five key-locations along the Portuguese coastline, considering projected digital terrain models, built upon the shoreline projections obtained in Part I. Future extreme total water levels are obtained through a probabilistic approach, and extreme wave events are defined considering high wave energy thresholds in a changing climate. Overall, extreme coastal flooding is projected across several urbanized sections along the Portuguese coastline, especially in areas without artificial protection infrastructures. Dune erosion is expected along the sandy stretches, reducing the natural protection against extreme coastal events up to 13.3%, and promoting widespread overtopping, leaving populations more exposed. Future projections reveal the episodic flooding of up to 1.47 km2 of land along the 14 km of analyzed coastline, threatening households and commercial hubs, besides services and communication routes. As physical and human losses may increase substantially in the future, our results call for the implementation of adequate coastal management and adaptation plans, strategically defined to withstand changes until 2100 and beyond.