​Nutraceuticals (NLs) are biomolecules (carbohydrate derivatives, polyphenolics and fatty acids/structural lipids, carotenoids) that have health-promoting, disease-preventing, or medicinal properties. NLs are found in small amounts in dietary sources, thus it is necessary to develop procedures to increase their concentration and extractability. The agri-food by-products could be appropriate for using them as raw materials in the production of these industrially relevant bioactive compounds under solid-state fermentation (SSF) conditions. The aim of the present project is to develop, for the first time in the field, improved SSF processes using encapsulated fungal spores (individual and mixed-cultures), with different functions/ properties/ biosynthesis mechanisms to enrich simultaneously some abundant agro-industrial by-products (brewer's spent grain and grape pomaces) with valuable hydrophilic (polyphenolics) and lipophilic (polyunsaturated fatty acids and β-carotene) biomolecules.