Industrial expansion has increased the use of volatile organic solvents for extraction processes, which, as well as the generation of contaminants that reach the effluents, cause health problems and damage to the environment. Most of the methods applied for wastewater treatment are insufficient to achieve the removal of toxic metabolites. The growing industrial development generates large quantities of agro-industrial by-products that have an exploitable composition of high value for the food industry that are sometimes not utilized due to the low solubility of some of their components. Ionic liquids (IL) are organic salts with melting points below 100 °C. This work analyzes their physicochemical properties in separation processes, as well as their industrial applicability and excellent extraction capacity which, combined with their low vapor pressure, makes them green solvents with tunable eco-friendly, biocompatible and biodegradable properties, promising for the extraction of compounds of interest for the food industry and wastewater treatment.