Secondary metabolites are ubiquitous substances occurring naturally in trees and microorganisms. They are produced in various metabolic pathways which determine their structure and biochemical proprieties. However, the biological functions of many secondary metabolites remain undetermined. Usually, the amounts of secondary metabolites produced by trees under natural conditions are limited, which makes their mass production difficult and not cost-effective. Metabolites occurring naturally in plants, including gymnosperm and angiosperm trees, as well as in fungi, are important biologically active substances used by many industries and in modern medicine. The huge variability and potential of biological activity present in secondary metabolites make it possible to replace most of them with compounds of completely natural origin. The current breakdown of metabolites, together with the most important examples of compounds and their uses, are presented in this overview. The possibility of increasing the number of secondary metabolites in a specific environment through interaction with the most known biotic factors is discussed. The use of in vitro culture for the production of secondary metabolites and their extraction, as well as the possibility of subsequent analysis, are described. The current literature on the metabolites produced by individual species is presented.