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Abstract The use of biopesticides based on Bacillus thuringiensis (Berliner 1915) in agriculture has been considered harmless for non-target organisms such as fish. The present study aimed to investigate the effects of a biopesticide based on B. thuringiensis on the physiology and histology of the liver, kidney and intestine of Arapaima gigas (Schinz, 1822), via exposure to water (0.13 g/L) and in the diet (0.13 g), after 24 and 48 h. Fish subjected to B. thuringiensis in the water of their breeding and feeding tanks exhibited mortality due to changes in erythrogram (hematocrit, hemoglobin, erythrocytes), thrombogram and leucogram blood parameters, and plasma (sodium, chloride, potassium, cholesterol, glucose, triglycerides, cortisol and total proteins) and enzymatic (Aspartate Amino Transferase and Alanine Amino Transferase) biochemistry. Histopathological alterations in the liver and kidney ranged from mild to severe and were characterized by the presence of cytoplasmic vacuolization, nuclear hypertrophy and atrophy, melanomacrophage centers and necrosis, and in the intestine by changes to the number of villi and goblet cells. Therefore, these physiological and histopathological alterations indicate that care should be taken with the dispersion of biopesticides based on agricultural B. thuringiensis in fish farming.