The sustainable use of residual lignocellulosic biomass is an opportunity to help to overcome the global need to reduce the emission of pollutants as well as depletion of fossil fuel resources and increasing energy demands. This study aimed to establish a deconstruction process of oil palm empty fruit bunches (EFBs), employing hydrothermal and biological pretreatments. Initially, the yields of cellulose, hemicellulose, lignin, extractives and ashes resulting from the autohydrolysis of raw EFBs were measured. The biological pretreatment of the raw EFBs followed using eight basidiomycetes strains. Finally, an enzymatic hydrolysis comparison between basidiomycetes and commercial enzymes evaluated glucose and xylose yields, the synergism degree and the reduction of phenolic substances. Autohydrolysis pretreatment presented the best sugar yields after hydrolysis. However, biological pretreatment provides enzymes and other advantages. The combination of enzymatic extracts of basidiomycetes with Celluclast and Novozyme‐188 Sigma® gave the best glucose yield with Flavodon flavus BRM‐055676 (14.78%). Synergism degree analyses showed an increase of 47% in glucose release by the cocktail of Fomes fasciatus BRM‐055675 with commercial enzymes. The deconstruction of EFBs by biological pretreatment presented a 2.96 ratio loss of lignin/loss of cellulose with F. flavus BRM‐055676. Finally, combinations of enzymatic extracts from basidiomycetes and ascomycetes, mainly F. fasciatus BRM‐055675, provided the reduction of phenolic substances. © 2021 Society of Chemical Industry and John Wiley & Sons, Ltd