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Pepper is a key agricultural crop susceptible to accumulating heavy metals like cadmium (Cd) and barium (Ba), posing significant health risks. To address these issues, this study investigated the effects of foliar applications of fulvic acid (FA), Zn-fulvic acid (Zn-FA), and Fe-fulvic acid (Fe-FA) on Ba and Cd uptake in pepper tissues, as well as their impact on nutritional quality, biomass, and leaf enzyme activity. Results indicated that Fe-FA application significantly reduced Cd and Ba in pepper fruit by 25 % and 93 %, respectively. Additionally, Fe-FA enhanced pepper growth, increasing vitamin C and phenolic compounds by 136 % and 13 %, respectively. Metabolomics analysis revealed that Fe-FA application up-regulated 857 metabolites and down-regulated 1045 metabolites. Furthermore, Fe-FA primarily influenced amino acid, carbohydrate, and lipid metabolism, promoting pepper growth. These findings suggest that Fe-FA foliar application offers a promising strategy for reducing Ba and Cd accumulation in pepper fruits while enhancing its nutritional quality.