Medicinal plants contain big numbers of phytochemicals that make them widely used in folk medicine and food industry as aroma and flavor additives. Fungal contamination may occur at pre-and post-harvest. In the current investigation twenty-three fungal species related to 11 genera were isolated from 30 samples of medicinal plants by using the dilution plate method. The results revealed that fungi were abundance in marjoram samples followed by rosemary, and thyme. The most frequent species were Aspergillus niger, A. flavus, Emericella nidulans, Penicillium chrysogenum, and Rhizopus stolonifer. Rosemary methanol extract was the only effective one against Escherichia coli with the highest inhibition diameter (13 mm). Thyme methanol extract achieved highly suppression of Candida tropicalis with the highest inhibition zone (31 mm). N-butanol extract of the selected plants did not display any antifungal efficacy except marjoram extract slightly inhibited the tested pathogenic fungi. Interestingly, the tested plants significantly inhibited the proliferation of breast and lung tumor cells and rosemary extract showed the highest cytotoxicity against human causian breast adenocarcinoma (MCF-7) followed by marjoram and thyme was the lowest with IC50: 8.9, 28.4, and 45.6 µg/ml, respectively. On the other hand, lung adenocarcinoma (A549) was highly inhibited by thyme extract then rosemary, and lastly, marjoram with (IC50: 33.7, 36.3, and 40.4 µg/ml, respectively). Fourier Transform Infrared (FTIR) analysis of rosemary residue discovered the existence of a greater number of effective compounds than thyme and marjoram.