Background: Endurance athletes require personalized nutrition strategies to optimize performance, recovery, and training adaptations. While traditional sports nutrition guidelines provide a foundation for personalization, individual variability in metabolic responses underscores the need for precision nutrition, tailored to genetic, biological, and environmental factors. This scoping review evaluates the application of systems biology-driven sports nutrition for endurance athletes, focusing on ‘omics’ and wearable technologies. Methods: A scoping review of the literature was conducted following PRISMA guidelines across PubMed, Scopus, and Web of Science with the following inclusion criteria: original research in English, involving endurance athletes, systems biology approaches, and nutritional interventions or continuous glucose monitoring (CGM). Relevant data were extracted in a systematic way. Results: Forty-eight reports were included with running as most studied sport. Eleven reports used metabolomics, ten nutrigenetics, nine metagenomics, nine CGM, six multi-omics, one proteomics, one epigenomics, and one lipidomics. Over half (62%) were randomized controlled trials (RCTs). Most studies were proof-of-concept investigations aimed at assessing biomarkers; however, the evidence linking these biomarkers to performance, recovery, and long-term health outcomes in endurance athletes remains insufficient. Significant inter-individual variability in responses to exercise and nutritional interventions was observed. Furthermore, many studies were constrained by small sample sizes and inadequate reporting of training status. Conclusions: While evidence is limited, some of the reviewed papers suggest a potential utility of systems biology-driven nutritional recommendations for endurance athletes. Future research should focus on well-powered replicated crossover RCTs, 360-degree systems-wide approaches, and validation of genetic impacts on nutritional interventions to refine dietary guidelines.