Increasing evidence points toward the critical and long-term involvement of prenatal and early nutrition and lifestyle on later health and disease risk predisposition. Metabolomics is now a well-established top-down systems biology approach that explores the genetic-environment-health paradigm. The generalization of such approaches has opened new research areas to deepen our current understanding of many physiological processes, as well as foods and nutrient functionalities in target populations. It is envisioned that this will provide new avenues toward preventive medicine and prognostic strategies for tailored therapeutic and personalized nutrition management. The development of systems biology approaches and the new generation of biomarker patterns will provide the opportunity to associate complex metabolic regulations with the etiology of multifactorial pediatric diseases. This may subsequently lead to the development of system mechanistic hypotheses that could be targeted with new nutritional personalized concepts. Therefore, this review aims to describe recent applications of metabolomics in preclinical and clinical fields with insights into disease diagnostics/monitoring and improvement of homeostasis metabolic regulation that may be translatable to novel therapeutic and nutrition advances in pediatric research.