Corals are fundamental elements of rocky shore coastal ecosystems, which are threatened by several local and global stressors including wastewater and river discharges, tourism and climate change. Among these, the impact of contaminants of emerging concern (CECs) still needs to be thoroughly investigated. The aim of this study was twofold: i) monitoring the health status of the Mediterranean zooxanthellate solitary coral Balanophyllia europaea in the Tyrrhenian Sea and ii) assessing sensitivity to polystyrene nanoparticles (PS NPs, 50 nm) and rare earth elements (Gadolinium, Gd) at low concentrations (10 µg/L–1 mg/L) on B. europaea adults (chronic, 28d) and larvae (acute, 48h, chronic, 28d). The natural population was monitored via mucus microbiome analysis and untargeted whole-organism metabolomics. Bench-studies on PS NPs and Gd ecotoxicity involved coral adults, evaluating mortality, predatory ability, photosynthetic efficiency, zooxanthellae count, pigment density and oxidative stress biomarkers, and coral larvae evaluating behaviour, mortality, metamorphosis and histological alterations. Results showed that both microbiome and metabolic profile were highly influenced by sampling times and environmental conditions. Bench-studies revealed no mortality in either larvae and adults, while acute Gd and PS NPs exposure caused a reversible alteration of larval swimming behaviour at 1 mg/L, and the chronic exposure caused structural depletion of surface cilia for PS NPs and 50% nonsense metamorphosis (metamorphosis without settlement) for Gd. Adults showed a mild reduction in photosynthetic pigments of zooxanthellae after 28 days with no alteration of photosynthetic efficiency and oxidative stress biomarkers. Overall data showed that larval swimming and adult mucus microbiomes provide effective, non-invasive indicators for early toxicity and wild coral health monitoring. Furthermore, these results emphasize the need to consider the vulnerability of early life stages in conservation strategies, highlighting how CECs can alter critical developmental processes in Mediterranean coral species.