Coffee industry produces large amounts of residues, mainly associated with roasting and consumption. Among these residues, coffee silver skin (CSS) and spent coffee grounds (SCG) are the most generated. In recent years, CSS and SCG have been object of increasing attention by researchers to study their possible reuses. The growing interest in the use of natural compounds has made it possible to study these residues as a source of bioactive compounds such as caffeine (CAF) and chlorogenic acids (CGAs). Nowadays, a great variety of techniques can be used for recovering of bioactive compounds from biomasses as raw materials. However, we need to evaluate more sustainable methodologies that, for instance, do not require the use of organic solvents. Accordingly, water is often accounted as the greenest solvent because of the its non-harmful character for both environment and human health. In our study, hydrodistillation (HD) process has been tested as a green method to recover and differentiate valuable compounds from SCG and CSS. HD is a variant of steam distillation in which the matrix is in direct contact with the solvent. In the present experiment, water has been chosen as a green solvent. Basically, the HD process allows merging the autohydrolysis extraction in mild temperature conditions (about 100°C), inside the boiler, with the continuous recovery of a condensate fraction with potentially different composition than the water-extract inside the boiler. In our experiment three matrices have been used, SCG, CSS and coffee powder as benchmark. Two fractions have been obtained, the condensate fraction, recovered in condenser column, and the water-extract, i.e. a phytocomplex recovered inside boiler. The two fractions of each processed matrix were characterized and then differentiated by chemical and physical analyses (total dissolved solids, electrical conductivity, oxidation-reduction potential and pH). Furthermore, compositional profiles were analyzed with HPLC technique, confirming the presence of compounds of interest such as caffeine and chlorogenic acids. In conclusion, the HD process allowed us to obtain two different fractions with different chemical and physical features, depending on the coffee residues (SCG and CSS). This could allow for a wider spectrum of possible uses of coffee residues available to the interested industry.