Different secondary metabolites (SMs) with novel biological properties, such as antifungal, antibacterial, antiplasmodium, cytotoxic, aggregation, antiplatelet, immunostimulant, enzyme-inhibiting, algicide, antitumor, anticancer, antiviral, and phytotoxic activities, are produced by microorganisms, algae, lichens, and plants. Secondary metabolites play an important role in interacting with the environment whereas, primary metabolites are present throughout the nature and are actively involved in the growth and development of plants. Terpenes are the largest class of secondary metabolites found in plants and are crucial for defence mechanisms against diseases and herbivores. Alkaloids, phenolics, and diterpenes are examples of plant secondary metabolites that have significant anticarcinogenic potential. Carotenoids serve as a pigment to absorb light during photosynthesis and offer photoprotection. Due to their ability as an allelopathic agent and phagostimulant, carotenoids are also effective in interacting with other organisms. Similarly, flavonoids are important for UV filtration, nitrogen fixation, flower coloration, and defences against a variety of illnesses. Plants are also protected by these secondary metabolites from various biotic and abiotic stressors. However, a large number of bioactive metabolites are also present in microorganisms, though not all of them. Alkaloids, terpenoids, polyketides, isoprenoids and non-isoprenoids, quinones, and other secondary metabolites are abundant in marine microorganisms. These metabolites work to reduce inflammation, kill germs, and fight tumors. Due to their antifungal and antibacterial activity against numerous diseases, secondary metabolites from fungus have significant medicinal importance. This chapter therefore offers an insight into bioactive metabolites produced by microorganisms and plants with their potential application in agriculture and/or medicine.