Chronic exposure to pesticide residues, even at low doses, significantly disrupts the intestinal microbiota, leading to dysbiosis characterized by a >50% reduction in beneficial bacteria (Lactobacillus, Bifidobacterium) and a proliferation of pathogens (Escherichia/Shigella, Clostridium). This imbalance is accompanied by altered production of short-chain fatty acids, leading to increased intestinal permeability, systemic inflammation and metabolic disturbances. These mechanisms contribute to the development of chronic diseases (obesity, type 2 diabetes). This review analyzes the impact of pesticides on the microbiota and their pathological implications, highlighting the need for tighter regulation to safeguard public health.