Medicinal and aromatic higher plants are sustainable resources for natural product compounds, including essential oils, phenolics, flavonoids, alkaloids, glycosides, and saponins. Extractives and essential oils as well as their bioactive compounds have many uses due to their antimicrobial, anticancer, and antioxidant properties as well as application in food preservation. These natural compounds have been reported in many works, for instance biofungicide with phenolic and flavonoid compounds being effective against mold that causes discoloration of wood. Additionally, the natural extracts from higher plants can be used to mediate the synthesis of nanoparticle materials. Therefore, in this review, we aim to promote and declare the use of natural products as environmentally eco-friendly bio-agents against certain pathogenic microbes and make recommendations to overcome the extensive uses of conventional pesticides and other preservatives.