Exposure to pesticide residues during the first 1000 days of life can disrupt body homeostasis and contribute to chronic metabolic diseases. Perinatal chlorpyrifos (CPF) exposure alters gut microbiota (GM) balance, potentially affecting offspring's health. Given the GM influence on brain function, the primary aim is to determine if pesticide-induced dysbiosis (microbial imbalance) affects indirectly other organs, such as the blood-brain barrier (BBB). The secondary objective is to evaluate the prebiotics protective effects, particularly inulin in promoting microbial balance (symbiosis), in both mothers and offspring. A total of 15 or more female rats were divided in 4 groups: control, oral CPF-exposed (1 mg/kg/day), exposed to inulin (10 g/L), and co-exposed to CPF and inulin from pre-gestation until weaning of pups. Samples from intestines, spleen, liver, and brain microvessels underwent microbiological and biomolecular analyses. Bacterial culture assessed GM composition of living bacteria and their translocation to non-intestinal organs. RT qPCR and Western blotting detected gene expression and protein levels of tight junction markers in brain microvessels. CPF exposure caused gut dysbiosis in offspring, with decreased Lactobacillus and Bifidobacterium and increased Escherichia coli (p < 0.01) leading to bacterial translocation to the spleen and liver. CPF also decreased tight junction's gene expression levels (50 to 60% decrease of CLDN3, p < 0.05). In contrast, inulin partially mitigated these adverse effects and restored gene expression to control levels. Our findings demonstrate a causal link between GM alterations and BBB integrity disruptions. The protective effects of inulin suggest potential therapeutic strategies to counteract pesticide-induced dysbiosis.