Taraxacum kok-saghyz (TKS) is a sustainable industrial crop traditionally cultivated for natural rubber production. However, its pharmaceutical potential remains underexplored. In this study, we present an integrated green analytical platform to simultaneously recover natural rubber and pharmacologically active secondary metabolites from TKS roots and leaves. Using UPLC-MS/MS, we identified 1,813 metabolites, including caffeoylquinic acids, flavonoids, and lipid derivatives. Multivariate analyses (PCA, OPLS-DA) confirmed tissue-specific metabolic specialization, revealing 964 differentially expressed compounds between roots and leaves. Notably, leaf tissues were enriched in cynarin, chicoric acid, and luteolin derivatives—compounds known for antioxidant, hepatoprotective, and neuroprotective effects. We implemented an ethanol–aqueous biphasic extraction to optimize compound preservation and co-extraction efficiency, validated via KEGG pathway mapping and mass spectrometric quantification. KEGG enrichment highlighted active biosynthesis of flavonoids and amino acid metabolites, supporting the nutraceutical relevance of TKS leaves. Root-specific enrichment of quinones and alkaloids suggests stress adaptation and antimicrobial potential. This study demonstrates the feasibility of developing a dual-use biomanufacturing platform for botanical APIs and clean latex from U.S.-grown TKS. It contributes to the standardization of metabolite recovery from non-model plants and supports domestic sourcing of high-value nutraceutical ingredients. Our green extraction methodology enhances reproducibility and analytical rigor in dietary supplement development.