A vast range of pesticides have been routinely employed for plant protection throughout the last few decades. Pesticides can enter non-target organisms in various ways, posing health hazards. Exposure to different environmental pollutants, including pesticides, can affect the human gut flora. Metabolites generated from the gut microbiota play an essential role in the host's health by regulating metabolic homeostasis. A disruption in this equilibrium can lead to the emergence of numerous illnesses and their etiology. Pesticides have been shown in a few recent studies to harm the host's gut microbiome. As a result, there is an urgent need to investigate the impact of pesticides on gut microbiota-mediated immunity. Metabolic alterations in the host may give a better understanding of pesticide-induced harm. This review highlights the potential consequences of pesticide exposure on gut microbiota composition and function, mainly focusing on how it might alter the production of secondary metabolites with potential downstream implications for host health.