Background: The decrease in the production of Argopecten purpuratus scallops in Chile is linked to extensive larval deaths in hatcheries caused by bacterial pathogens, particularly Vibrio genus, threatening sustainability. Traditional antibiotic practices raise concerns, urging research on eco-friendly strategies like bacterial probiotics. This study explores the metabolic responses of scallop larvae to Vibrio bivalvicida and evaluates the impact of the Psychrobacter sp. R10_7 probiotic on larval metabolism pre- and post-infection. Materials and Methods: Analysis detected 183 metabolite features, revealing significant changes in larval metabolites during Vibrio infection. Larvae pretreated with probiotics showed a metabolic profile comparable to non-infected larvae, indicating low impact on larval metabolome, likely due to probiotics antagonistic effect on pathogens. Results: Arachidonic acid, eicosatrienoic acid, docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and docosapentaenoic acid (DPA) were significantly higher in non-pretreated/infected larvae compared to both pretreated/infected and non-pretreated/non-infected larvae, potentially supporting the activation of immune response in non-pretreated larvae to Vibrio infection. Identification of 76 metabolites provided insights into scallop larvae metabolome, highlighting the enriched metabolic pathways associated with energy provision and immune response. Conclusions: Probiotic pretreatment may mitigate metabolic disruptions in scallop larvae caused by Vibrio infection, suggesting a promising strategy for sustainable scallop production.