The constituents of the hydroethanolic extract of Azadiracta indica root were investigated using ultra-performance liquid chromatography-quadrupole-time-of-flight mass spectrometry (UPLC-QTOOF-MSE). Acute toxicity was evaluated in an experimental animal model. We investigated the antibacterial activities of A. indica roots against Salmonella typhimurium and Staphylococcus aureus and the antifungal activities against strains of Trichophyton rubrum, Candida albicans and Candida tropicalis. We identified nine secondary metabolites in the hydroethanolic extract by UPLC-QTOOF-MSE. The extract was highly effective in inhibiting the growth of T. rubrum strains, so it can be effective in combating the dermatophyte tested, but it had no inhibition potential on any bacterial strains or Candida species evaluated. It was possible to infer that the extract had no acute toxicity in relation to the animal model Danio rerio. Therefore, since neem has a high bioactive potential and adapts well to the climate of semiarid regions, growing this species could become a source of income for farmers by its use to produce naturals fungicide and drug, as alternatives to conventional products, which can cause microbiological resistance and/or are toxic to the environment, besides being expensive.