Secondary metabolites (SMs) are natural compounds produced mainly by bacteria, fungi, and plants. They are low molecular weight compounds that have a wide range of chemical structures and biological functions. Secondary metabolites are so named because, unlike primary metabolites such as lipids, amino acids, carbohydrates, and nucleic acids, their synthesis is not required for the organism’s development and reproduction. Today, the production of secondary metabolites is an important area of research for organic chemists, molecular biologists, and bioinformaticians. In this research, two types of secondary metabolites produced by plants, such as alkaloids and flavonoids, were studied and information was collected on the types of compounds, structures, biological activities, and commercial applications of these two types of secondary metabolites.