The antipsychotic chlorpromazine (Cpz) has raised concern as a pharmaceutical effluent due to its wide medical applications. Moreover, its potent pro-oxidant properties and impact on the cell viability of the marine mollusc Mytilus galloprovincialis, even at low concentrations (ng/L), have been noted. Based on this evidence, in this study, we investigated the physiological effects of Cpz on M. galloprovincialis, to elucidate its fate within the organism, in terms of bioaccumulation, biotransformation, byssus changes and stress responses of the cellular thiolome. Histological and indicators of vitality analyses were also performed to better evaluate the influence of the drug on the morphology and cell viability of the digestive gland. To this end, two different concentrations of Cpz (Cpz I (12 ng/L or 37 pM) and Cpz II (12 μg/L or 37 nM)) were administered to mussels over 14 days. Cpz accumulation in the digestive gland significantly increased with water concentration (BCF of Cpz I and Cpz II). Biochemical analyses indicated lysosomal dysfunction, reflected in elevated total Cathepsin D activity and compromised lysosomal membrane stability. Stress-related and metal-buffering proteins (GST and metallothionein) responded to both Cpz concentrations. Cpz I induced phase I biotransformation activity (CYP450-dependent EROD), while Cpz II triggered caspase-3 activation, indicative of detoxification overload. Histological analysis revealed digestive gland atrophy, epithelial thinning, haemocyte infiltration, and brown cell presence. Byssus analysis showed significant alterations. In conclusion, our study underscores Cpz-induced physiological and histological changes in M. galloprovincialis, posing potential implications for mussel health and confirming the utilisation of this mussel as an indication of Cpz ecotoxicity.