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We substituted 10% of fishmeal with scallop (Argopecten ventricosus) or squid (Dosidiscus gigas) by‐product meal in a feed for shrimp (Litopenaeus vannamei) growth assay that lasted 60 days and then shrimps were submitted to handling stress. Shrimp fed the control diet had smaller weight gain and lower recovery after stress. Prostaglandins in gills were affected by diet and stress, with significant differences in shrimp fed the control diet before and after the stress. Hydroperoxides were increased after stress, while isoprostanoids were higher in shrimp fed the control diet. The gene expression of Glutathione peroxidase and Catalase was increased on the stressed shrimp fed the scallop diet, with no differences among diets for Superoxide dismutase or Cyclooxygenase. Arachidonic acid in the phospholipid fraction of muscle was the only fatty acid affected by stress and diet. Cholesterol oxidation products were significantly higher in shrimp fed the scallop diet compared to shrimp fed the control diet before applying the stress. A PCA analysis grouped in one‐factor growth variables, as well as Superoxide dismutase, esterified astaxanthin and isoprostane, while another factor was determined by stress, prostaglandin and hydroperoxide levels in gills. The partial substitution of fishmeal with scallop of squid by‐product meals affected growth and stress differently, indicating shrimp that grew up more were not necessarily more tolerant to handling stress, which can have a strong repercussion in aquaculture, particularly during density control, recording of growth and harvest. [ABSTRACT FROM AUTHOR]