The emergence of microbial resistance to antimicrobial agents emphasizes the need to discover new ones. The potential use of endophytic fungi as a source of antimicrobial agents and their mode of action has not been fully explored. Thus, this research aimed to evaluate the antimicrobial activity of 16 endophytic fungal species isolated from some plants collected from Wadi Hagul, Egypt, along with assessing the mechanism of action of the most active one. Alternaria E15 was the most effective fungus against S. aureus with an MIC of 321.5 μgmL−1, E. coli, A. niger with MICs of 1250 μgmL−1, and C. albicans with an MIC of 2500 μgmL−1. It was identified morphologically and molecularly as Alternaria alternata (accession no. PX106371). Sorbitol protection and ergosterol-binding assays indicated that its ethyl acetate extract does not target the fungal cell wall but acts through direct ergosterol binding in the fungal membrane. LC/MS analysis of A. alternata extract revealed seventeen major compounds belonging to different antimicrobial chemical classes. The docking studies on CYP51 and Penicillin-Binding Protein 3 showed that Okanin4-(6-acetylglucoside) and alternariol (docking scores −11.957 and − 7.009, respectively) may inhibit fungal ergosterol biosynthesis, while Okanin4-(6-acetylglucoside) and altenusin may inhibit bacterial cell wall synthesis (docking scores −8.537 and − 8.019, respectively). This study highlights, for the first time to our knowledge, the investigation of Egyptian endophytic fungi isolated from certain plants as a potential source for antimicrobial products, with an understanding of the responsible compounds and their mechanisms supporting their potential use in developing novel medicinal applications.
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