Biocatalysis is a green and sustainable technology based on the use of natural substances to catalyze chemical reactions. Humans have been unconsciously using biocatalysis for thousands of years to produce food and alcoholic beverages, but it is only since the 19th century that we have begun to understand its fundamentals and its enormous potential. In fact, advances in our knowledge of enzymes and metabolic pathways and, in recent decades, the introduction of tools such as bioinformatics, DNA sequencing and protein engineering have made biocatalysis a key strategy in fine chemistry and for the production of active pharmaceutical ingredients. In addition, the discovery of new microorganisms adapted to adverse conditions has also been crucial in advancing this avenue. The present review focuses on the use of unconventional yeasts and their enzymes in the most interesting reactions where biocatalysis is applied. It highlights the advantages of using these microorganisms in industrial chemical processes due to their particular phenotypes, such as their ability to withstand high temperatures and pressures, as well as acidic or alkaline environments, high substrate loads, presence of organic solvents, etc. All this results in a wider range of possible substrates and higher efficiency. Examples of the most important reactions in which their use has been described are included, considering both catalysis by wild-type whole cells or their isolated enzymes and their genetically modified variants. All this information will help to understand the current relevance of unconventional yeasts and their enzymes in biocatalysis.