Early larval stages of marine bivalves are highly sensitive indicators of environmental contamination, yet the distinct impacts of microplastics and chemical pollutants on morphogenesis and biomineralization remain poorly characterized. This study evaluated the effects of environmental microplastics (EMPs), diuron, and their mixture on Mytilus galloprovincialis larvae at environmentally relevant concentrations. Using an integrative approach, we assessed embryotoxicity (larval abnormalities and growth), shell calcium deposition, tissue integrity (histology and polarized light microscopy (PLM)), and transcriptional responses of key genes involved in cytoskeletal stability (tubulin), shell formation (hrg), and calcium homeostasis (calreticulin). Exposure to diuron markedly increased larval abnormalities (56.8 ± 0.7%), particularly shell deformities and developmental arrest, whereas EMPs exhibited 42.7 ± 0.9% abnormal individuals, moderate growth inhibition, and mainly mantle anomalies. MIX exposure further exacerbated these effects, resulting in the highest embryotoxicity (62.9 ± 0.75%). Calcium deposition was significantly reduced under diuron (174.32 ± 1.26) and MIX (163.61 ± 5.23) treatments, whereas EMPs (180.45 ± 8.44) had a milder effect, confirming that biomineralization is differentially sensitive to chemical and particle stressors. Histological and PLM analyses revealed that diuron primarily impaired shell mineralization, EMPs disrupted mantle architecture, and MIX induced combined structural and mineralization defects. Gene expression patterns mirrored these observations, indicating stressor-specific modulation of biomineralization, cytoskeletal organization, and calcium regulation. Overall, our findings demonstrate that chemical and particle stressors differentially target critical cellular processes involved in morphogenesis and biomineralization, yet ultimately converge on impaired shell formation. This integrative framework provides mechanistic insight into early larval vulnerability and supports the use of multi-level biomarkers to predict sublethal effects on recruitment and population resilience in polluted coastal ecosystems.