Microwave assisted extraction is used to extract compounds from matrices, such as oils and other volatile natural products from plant matter. It can be used for both testing and routine extraction in areas including food testing, biofuel and medicine production, and the environmental analysis of soils, sludge and waste matter. Methods such as microwave assisted extraction and Soxhlet extraction are used when the compound to be extracted has limited solubility in a solvent and the impurity is insoluble in the solvent. The rapid heating that microwaves produce allows rapid extraction of even thermally unstable substances. It also reduces the use of solvents and in some cases can enable solvent free extraction.

A Soxhlet extractor works by cycling the solvent through the plant matter, while simultaneously evaporating the resulting solution, to progressively increase the concentration of the compound to be extracted while condensing the solvent vapor so it can be reapplied to the plant matter. Microwave assisted extraction uses the same principle but by rapid and selective heating it can more rapidly partition the compound to be extracted from the matrix into the solvent.

Microwaves heat samples in a fundamentally different way to classical conductive heating. Microwave energy causes heating by rotating molecular dipoles and through ionic conduction. Microwaves pass through solid matter, heating the entire sample simultaneously, quite unlike conductive heating in which heat propagates from the heated exterior. The rapid heating that microwaves cause can allow liquid solvents within closed vessels to be heated will above their normal boiling point, which further enhances extraction. There may also be advantages related to cell rupture and diffusion, resulting in greater yield.

Simple analytical-scale microwave assisted extraction systems may simply heat closed test tubes containing the sample and solvent in an oven. More advanced or higher-throughput systems may enable solvent cycling, as in Soxhlet extraction, combined with microwave heating.