White-rot basidiomycetes are the only microorganisms with the ability to produce both hydrolytic (cellulases and hemicellulases) and oxidative (ligninolytic) enzymes for attacking cellulose/hemicellulose and lignin, while they are also capable of degrading (oxidizing) a wide range of aromatic or toxic compounds. In addition, they produce secondary metabolites with important applications in the cosmetics industry. In the present work, three wild indigenous strains of Basidiomycete fungi (Pleurotus citrinopileatus, Abortiporus biennis and Ganoderma lucidum) were grown in different cultivation media (basal media and agroindustrial residues, such as olive oil mill wastewater, and corn cob). The cultures were examined in regard to the production of biotechnologically relevant enzymes and bioactive compounds. All strains were found to be preferential lignin degraders, in agreement with most known white-rot fungi. Bioinformatic analyses were performed on the proteome of the strains P. citrinopileatus and A. biennis, focusing on CAZymes with biotechnological relevance, and the results were compared with the data from the enzyme activities in the culture supernatants. In terms of secondary metabolism, compounds production and bioactivity of the extracts have been evaluated in relation to the different types of culture media. Principal components analysis (PCA) and volcano plots were generated based on ultra-high-performance liquid chromatography - high resolution mass spectrometry (UHPLC-HRMS) data to reveal significant variations in bioactive compounds amongst the extracellular fluids and fungal biomasses of pilot cultures. Overall, all three Basidiomycete strains were shown to be potent producers of secondary metabolites, but also of oxidative enzymes of special interest for biomass conversion applications.