Vegetable oils are hydrophobic compounds, such as tryacylglicerols and essential oils extracted from plants that have been used by humans for centuries in many different areas. The use of isolated enzymes and microorganisms applied to vegetable oils has been shown to be very interesting from an industrial viewpoint, due to the broad variety of products that may be obtained from it. As an example, biodiesel can be obtained through transesterification of vegetable oils, such as soybean and rapeseed oils, catalyzed by free and immobilized lipases from different microorganisms, including Candida antarctica and Pseudomonas fluorescens, with a conversion rate of more than 90% according to some studies. This is of great interest considering the current scenario of biofuels and environmental consciousness. Lipases from microorganisms such as Mucor miehei and Candida antarctica have also been studied for the production of structured lipids through interesterification reactions, using vegetable oils and any other oil of interest to be incorporated as substrates such as conjugated linoleic acid. These modified lipids are attractive since they present improved therapeutic or technological properties compared to natural vegetable oils. Furthermore, lipases can be used as biocatalysts in the production of useful biodegradable compounds, using vegetable oils as substrates, including the production of 1-butyl oleate from direct esterification of butanol and oleic acid, to decrease the viscosity of biodiesel in winter use. Another example is the mixture of 2-ethyl-1-hexyl esters that can be obtained efficiently by enzymatic transesterification from rapeseed oil fatty acids, for use as a solvent. On the other hand, compounds of essential oils can be biotransformed by microorganisms to obtain high value-added compounds. Penicillium sp. has been studied for the biotransformation of R-(+)-limonene into R-(+)-α-terpineol, a compound with a floral and typically lilac odor that can be used as an aroma compound in many products. Additionally, metabolic engineering of plants to obtain high levels of oils with industrially desired properties, such as reduced viscosity, freezing point and calorific value, has been recently studied. Therefore, vegetable oils and biocatalysis represent a promising strategy in overcoming environmental issues and being economically viable. Many efforts must be made in order to understand the biological conversion and the development of new technologies. This chapter focuses on vegetable oils with particular emphasis on the use of enzymes and microorganisms for their modification in order to produce industrially relevant compounds.