So far, several studies have focused on the synthesis of metallic nanoparticles making use of extracts from the fruit of the plants from the genus Capsicum. However, as the fruit is the edible, and highly commercial, part of the plant, in this work we focused on the leaves, a part of the plant that is considered agro-industrial waste. The biological synthesis of gold (AuNPs) and silver (AgNPs) nanoparticles using aqueous extracts of root, stem and leaf of Capsicum chinense was evaluated, obtaining the best results with the leaf extract. Gold and silver nanoparticles synthesized using leaf extract (AuNPs-leaf and AgNPs-leaf, respectively) were characterized by UV-visible spectrophotometry (UV-Vis), Fourier Transform Infrared Spectroscopy with Attenuated Total Reflection (FTIR-ATR), X-ray Photoelectron Spectroscopy (XPS), Ultra Hight Resolution Scanning Electron Microscopy coupled to Energy-Dispersive X-ray spectroscopy (UHR-SEM-EDX) and Transmission Electron Microscopy (TEM), and tested for their antioxidant and antimicrobial activities. In addition, different metabolites involved in the synthesis of nanoparticles were analyzed. We found that by the use of extracts derived from the leaf, we could generate stable and easy to synthesize AuNPs and AgNPs. The AuNPs-leaf were synthesized using microwave radiation, while the AgNPs-leaf were synthesized using UV light radiation. The antioxidant activity of the extract, determined by ABTS, showed a decrease of 44.7% and 60.7% after the synthesis of the AuNPs-leaf and AgNPs-leaf, respectively. After the AgNPs-leaf synthesis, the concentration of polyphenols, reducing sugars and amino acids decreased by 15.4%, 38.7% and 46.8% in the leaf extract, respectively, while after the AuNPs-leaf synthesis only reducing sugars decreased by 67.7%. These results suggest that these groups of molecules are implicated in the reduction/stabilization of the nanoparticles. Although the contribution of these compounds in the synthesis of the AuNPs-leaf and the AgNPs-leaf was different. Finally, the AgNPs-leaf inhibited the growth of S. aureus, E. coli, S. marcescens and E. faecalis. All of them are bacterial strains of clinical importance due to their fast antibiotic resistance development.