The human body hosts a diverse community of microorganisms, with the gastrointestinal tract being the most densely colonized, hosting a thousand microbial species collectively referred to as the gut microbiota. Recent studies have demonstrated that the gut microbiota maintains multidirectional and communicational connections with various organs through metabolic, endocrine, neural, humoral, and immunological pathways. Alterations in this gut--organ axis can lead to a wide range of health issues beyond gastrointestinal disorders which affect other organ systems. Emerging evidence highlights the intricate relationship between diet and microbiota in the onset and progression of diseases. Personalized nutrition has gained attention as a strategy to identify specific microbiome traits that predict responses to dietary components. This approach holds promise for designing targeted dietary interventions that promote favorable health outcomes by modulating the gut microbiota. This systematic review explores current insights into the mechanisms underlying gut--organ interactions and examines the potential of personalized nutrition for disease prevention taking advantage of these mechanisms. Furthermore, it addresses existing limitations in understanding the mechanistic pathways and the implementation of personalized nutrition as a preventive strategy. Finally, by summarizing the latest findings, this review aims to provide a clearer understanding of the gut microbiota's role in systemic health and its modulation through dietary strategies, paving the way for innovative approaches in preventive medicine.