Endophytic microorganisms are considered as a promising source for the production of bioactive secondary metabolites to treat the drug resistant microbes. Fifteen fungal isolates were isolated from four ornamental plants grown in Egypt namely; Ricinus communis, Hibiscus rosa-sinensis, Morus alba and Ficus nitida. The fungal isolates were screened for their ability to produce bioactive secondary metabolites by cultivating them on rice medium for 14 days. The metabolites were extracted by ethyl acetate followed by acetone. The obtained extracts were tested for their antimicrobial activities. Scale-up fermentation was performed for three promising fungal strains isolated from Ricinus communis and Hibiscus rosa-sinensis. Antioxidant activities, total phenolic content, anticancer activities as well as GC/Mass studies were carried out for their extracts. The isolated fungal strains under investigation were identified using the molecular technique 18SrRNA. The fungal isolates were identified as Alternaria tenuissima isolate ANAS-9, Phoma herbarum isolate ANAS-10 and Aspergillus tamarii ANAS-13 with accession numbers MW662645, MW662651 and MW662652, respectively. High total phenolic content, potent antioxidant and Gram+/- antimicrobial as well as antifungal activities have been evidenced for the three new isolates. Both ANAS-9 and ANAS-10 had very strong anticancer effect on liver (HepG2) and breast (MCF-7) cancer cell lines, while ANAS-13 reported moderate cytotoxicity against both of them. This study concluded that these fungal strains have potent biological activities for the treatment of multidrug resistance pathogenic bacteria, as well as anticancer and anti-inflammatory agents' production.