The aims of this work were to isolate fungal strains from agriculture soil samples, to screen their antimicrobial and antiaflatoxigenic activity, to identify and evaluate the antimicrobial and antioxidant activity of their bioactive potential secondary metabolites. Five fungal strains were isolated from soil samples collected from different areas in Mansoura, Dakahlia governorate, Egypt. Only two of the isolated fungal strains showed high antimicrobial activities against several microbial pathogenic microorganisms and they also showed antiaflatoxigenic activities. These promising isolates were identified using molecular identification technique as Aspergillus niger and Aspergillus fumigatus. Bioactive secondary metabolites were extracted from these fungal species and showed strong antimicrobial activity against several microbial pathogens, as well as variable antioxidant properties and total phenolic content. Twenty-six compounds were identified from the ethyl acetate extracts of the mycelia of the shaken culture broth of Aspergillus niger by Gas Chromatography-Mass Spectrometry analysis. It could be concluded that the two fungal species isolated from the Egyptian environment and their crude extracts may be considered promising candidates for food application due to their antimicrobial, antioxidant and total phenolic content.