Global anthropogenic oceanic noise caused by shipping is predicted to double every 11.5 yr, putting marine organisms at risk. While the impact of noise on marine mammals is well documented, its effects on molluscs, which hold immense economic and ecological importance, remain largely unknown. To investigate the consequences of noise on mollusc metabolism during crucial early life stages, blue mussel Mytilus edulis larvae were exposed to shipping noise in a laboratory setting until the post-larval stage and their metabolome was analysed. Multivariate analyses of the metabolome showed that shipping noise induced stress-related inflammation with increased energy demand, higher protein turnover, and disrupted nervous system activity. Consequently, noise promoted delayed metamorphosis in suboptimal habitats with greater metabolic costs, which may affect ecosystem and aquaculture sustainability as competent mussel larvae struggle to select suitable development habitats. Without action to limit underwater noise, such impacts could disrupt population structures and marine biodiversity.