The widespread occurrence of microplastics (MPs) and endocrine-disrupting compounds as bisphenol A (BPA) poses risks to aquatic life. This study evaluates the effects of polystyrene (PS) MPs and BPA, individually and conjugated, on embryonic development of black sea urchin Arbacia lixula, an ecologically relevant bioindicator. Embryos were exposed to 1 and 5 µm PS MPs (10 µg/mL), BPA (5 and 25 µM), and BPA-sorbed PS MPs. A multi-endpoint approach was employed, integrating embryotoxicity assays, morphological evaluation, metabolomics, and enzymatic biomarkers of oxidative stress and neurotoxicity. Size-dependent accumulation of PS MPs was observed. BPA caused pronounced skeletal abnormalities and developmental arrest, whereas when adsorbed onto MPs exhibited mitigated toxicity, even with a higher internalization of particles. Metabolomics revealed significant alterations in neuromodulatory, energetic, and osmoregulatory pathways in all treatments. Similarly, enzymatic assays indicated redox imbalance and inhibited acetylcholinesterase activity. While both PS MPs and BPA, alone and conjugated, induced impaired embryogenesis, no synergistic effect between the toxicants was observed, likely due to the low sorption capacity of BPA on PS MPs. The absence of a synergistic effect between PS MPs and BPA suggests that, under the tested acute exposure conditions, microplastics may modulate rather than exacerbate BPA toxicity. Nonetheless, their co-occurrence can influence exposure routes and developmental processes, with relevant ecological implications for marine invertebrate early life stages. Therefore, even weak and transient particle-pollutant interactions can modulate contaminant behaviour and toxicity, reinforcing the need to incorporate adsorption/desorption dynamics rather than mixture scenarios into environmental hazard assessments of emerging pollutants.