American (Anguilla rostrata) and European (Anguilla anguilla) eel populations are declining since the 1980s, and contamination is thought to play a role. To determine the influence of organic (organochlorinated pesticides (OCPs), polybrominated diphenyl ethers (PBDEs), polychlorinated biphenyls (PCBs)) and inorganic (Zn, As, Cd, Cu, Pb, Cr, Ni, Ag, Se, Hg) contaminants on wild yellow eels liver and muscle metabolic capacities, enzymatic assays were performed. In A. rostrata liver, G6PDH moderate negative correlations with Ag, Pb, and As suggest impacts on lipid metabolism, and correlations between Cd and age (positive) and between Cd and relative condition factor (Kn; negative) indicate impacts on older eels health. Anguilla anguilla liver proteins, pyruvate kinase (PK), and lactate dehydrogenase (LDH) were positively linked to Zn, Pb, and Cu, suggesting effects on glycolytic and anaerobic capacities. In A. anguilla muscle, absence of correlation between age and lipids plus strong positive correlations between age and OCPs, PBDEs, PCBs, and Hg suggest lipid storage impairment in older contaminated eels. Overall, our study indicates contamination impacts on both species’ metabolic capacities, but the broader range of contaminants found in A. anguilla brings greater impacts compared with A. rostrata.