Age-related macular degeneration (AMD) and other retinal degenerative diseases are linked to oxidative stress resulting from chronic iron overload, excess lipids, and the phagocytic removal of the photoreceptor outer segments (POS) by the retinal pigment epithelium (RPE). The aim of this study was to identify important metabolic pathways and candidate metabolites that are altered by iron and lipid-mediated oxidative stress in human iPS-RPE cells, potentially offering targets for therapeutic intervention. Human iPS-RPE cells were treated with ferrous sulfate (FeSO4) alone, or FeSO4 together with low-density lipoprotein (LDL) or POS, and analyzed by untargeted metabolomics and pathway enrichment (MetaboAnalyst). Results showed that iron treatment greatly perturbs cellular metabolism, particularly in pathways of nitrogen and amino acid processing. The metabolites trigonelline, D-arabinose, and glyceric acid exhibited the largest changes, which suggest significant contributions to iron-induced cellular response. Trigonelline levels were significantly increased by iron in combination with POS, suggesting trigonelline may be a protective metabolite that can enhance antioxidant and amino acid synthesis pathways. These data define metabolic signatures of RPE susceptibility and resilience, and identify metabolites, including trigonelline, that could be therapeutically replaced to prevent oxidative stress-induced retinal degeneration.