Carotenoids are secondary metabolites involved, in animals, in the prevention of several animal diseases including cancers and cardio-vascular pathologies. In plants, they play essential functions as photosynthetic pigments in leaves, secondary metabolites in fruits and flowers, and hormone precursors; three out of them (α-/β-carotene, β-crypthoxanthin) cover a fundamental role in human nutrition as precursors of vitamin A. During last 20 years, we have generated a large collection of tomato and potato transgenics enriched in β-carotene and total carotenoids; within them, we have focused our attention on “golden” genotypes, including potato tubers expressing simultaneously three genes of bacterial origin (CrtB, phytoene synthase; CrtI, phytoene desaturase; CrtY, lycopene β-cyclase), and tomato transgenic fruits overexpressing lycopene beta-cyclase (LCY-b), beta-carotene hydroxylase (CHY) or both transgenes. We have performed a global profiling at transcriptional (microarray, next-gen sequencing), metabolomic (GC-/LC-MS) and phenomic level on all these materials. Integration of Gene expression profiles, integrated and high-throughput metabolomics, revealed unscheduled transcript-metabolite correlations and shed light on novel co-regulatory dynamics which emerged in berry ripening or tuber aging during post-harvest storage. A strong influence of carotenoid accumulation on fruit ripening kinetics was observed, probably mediated by the hormones ABA and ethylene, while GO enrichment analysis allowed identification of gene classes specifically regulated in "Golden" fruits. Networks of biological interactions and correlations have been employed to visualize and predict the consequences of metabolic engineering approaches on the whole plant metabolism. Overall, these analyses revealed the central role of carotenoids in regulating both fruit and tuber development and large-scale network analysis proved to be a valuable approach for rational design of new biofortified crops by through identification of higher correlative power nodes (hubs of the network), as potential targets in future breeding programs.