Diet is a well-known, modifiable factor that can either promote renal health or accelerate the onset and progression of chronic kidney disease (CKD). Advances in multiomics, particularly proteomics and metabolomics, have significantly enhanced our understanding of the molecular mechanisms linking diet to CKD risk. Proteomics offers a comprehensive analysis of protein expression, structure, and interactions, shedding light on how nutritional factors regulate cellular processes and signaling pathways. Meanwhile, metabolomics provides a detailed profile of low-molecular-weight compounds, encompassing both endogenous metabolites and diet-derived molecules, offering valuable insights into the systemic metabolic states that influence kidney function. This review explores the potential of proteomic and metabolomic analysis in identifying molecular signatures identified in human and animal biological samples, such as blood plasma, urine, and, in kidney tissues. These signatures are associated with the intake of specific foods and food groups, as well as overall dietary patterns, which may either contribute to or mitigate the risk of diet-related CKD. By elucidating these complex relationships, such research holds promise for advancing precision nutrition strategies aimed at preserving kidney health.