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The current study biosynthesized silver nanoparticles (AgNPs) using two fungal endophytes isolated from two Egyptian dangerous plants, Amaranthus viridis (Amaranthaceae) and Lotus corniculatus (Fabaceae). The fungal isolates were identified using traditional methods, and the 18S rRNA gene sequence was used to confirm the identification. With average particle diameters of 15–27 nm for Alternaria alternata and 11–21 nm for Aspergillus niger, respectively, fungal strains produced spherical AgNPs. In the UV-Vis spectra, the absorption peaks of AgNPs ranged from 459–462 nm. FT-IR spectra prove the existence of proteins as capping agents in AgNPs. Antimicrobial experiments revealed that AgNPs inhibited the growth of strains of fungi (Candida albicans and Aspergillus niger) and strains of harmful bacteria (Staphylococcus aureus, Bacillus cereus, Escherichia coli, and Pseudomonas aeruginosa). Cell wall lysis, distortion, and the distinction between the plasma membrane and the cell wall were all visible in transmission electron microscopy (TEM) micrographs of AgNPs-treated bacterial strains, as was complete cell lysis. In addition, AgNPs-treated fungal strains had a large gap between the plasma membrane and the cell wall, as well as lysed cell walls and severe plasmolysis in the protoplasm of the fungal cell. The findings suggest that in the future, bio-produced AgNPs might be used as efficient antibacterial and antifungal agents.