Purpose: The widespread consumption of potatoes is attributed to their easy availability and affordability. While potatoes provide numerous benefits, concerns arise due to their high carbohydrate content, often associated with health issues like obesity and diabetes. Nevertheless, they are rich in health-promoting compounds such as ascorbic acid, vitamins (C, B3, B6), proteins, minerals, and dietary fibers. Resistant starch, found in potatoes, acts as a beneficial nutrient for the gut microbiome. However, pesticides are commonly used during potato crop cultivation to combat diseases like mildew. Additionally, sprouting inhibitor treatments are employed for extended potato storage. Despite the known health hazards associated with pesticides, limited research has been examined on the combined effect of pesticide mixtures within food matrices. This study aims to explore the influence of pesticide treatments during crop cultivation and sprouting inhibitor treatments during storage, on the gut microbiota population and hepatic gene expression. Methods: Lyophilized bio or conventional potato with or without sprouting treatment or water was administered through orogastric gavage in mice over a 3-week period. Then, mice were euthanized to collect organs like the liver. Feces were collected before the initial gavage and after 3 weeks of gavage. Nutrigenomic analysis was conducted on liver RNA, and metagenomic analysis was performed on feces. Results: Findings from this study demonstrated notable modifications in gut microbiota and liver gene expression in mice following the consumption of potato bio or conventional, with or without storage (sprouting inhibitor treatment). Conclusion: This study highlights the effect of pesticide treatment and storage of potato on both gut microbiota population and gene expression modulation in the liver.