The electron beam irradiation (EBI) of native lignin has received little attention. Thus, its potential use in lignin-based biorefineries is not fully understood. EBI was applied to selected lignin samples and the structural and chemical changes were analyzed, revealing the suitability, limitations, and potential purpose of EBI in wood biorefineries. Isolated milled wood, kraft, and sulfite lignin from beech and eucalyptus were subjected to up to 200 kGy of irradiation. The analysis included gel permeation chromatography for molar masses, heteronuclear single quantum coherence (HSQC)- and 31P NMR and headspace gas chromatography-mass spectrometry for functional groups, and thermogravimetric analysis for thermal stability. Most samples resisted irradiation. Subtle changes occurred in the molecular weight distribution and thermal stability of milled wood lignin. EBI was found to be a suitable pretreatment method for woody biomass if the avoidance of lignin condensation and chemical modification is a high priority.