Within the biorefining concept, the lignocellulosic biomass wastes can serve as feedstock to produce value-added chemicals and fuels. The sustainable valorization of biomass is based on integrated processes that aim to the utilization of “whole biomass”. To this end, the first step of the efficient biomass pretreatment towards selective isolation of cellulose, hemicellulose and lignin, is of paramount importance. Hydrothermal pretreatment of biomass in neat water is a green and well-established process that enhances hemicellulose removal and recovery in the liquid fraction, affording a cellulose and lignin enriched solid which can be enzymatically hydrolyzed to glucose. A simple and efficient method to facilitate the hydrolysis is the prior extraction of the formed “surface” lignin which hinders the action of enzymes. Within this context, in this work, forestry (beechwood sawdust) and agro-industrial (vine prunings, apricot kernel shells) wastes were hydrothermally pretreated in neat water (at 220 °C, 15 min) and the formed surface lignin was extracted via soxhlet or reflux methods under mild conditions, with the use of green solvents (ethanol, acetone). The delignification degree of the pretreated biomass was in the range of 35–67 wt%, depending on the solvent and biomass feedstock. The recovered surface lignins were of high purity and exhibited similar physicochemical and structural characteristics with the organosolv lignin. The fast pyrolysis of surface lignins afforded bio-oils enriched in alkoxy-phenols and oxy-aromatics. The biomass solids recovered after lignin extraction are enriched in cellulose (70%) and exhibit high relative crystallinity and improved textural properties, thus increasing their potential valorization.