Hydrothermal liquefaction (HTL) is a wet thermo-chemical biomass conversion technology for the production of, e.g., liquid transportation fuels. The process yields a bio-crude with properties similar to petroleum crude but also with significant differences. Particularly the higher heteroatom content and high viscosity render bio-crudes unsuitable for a direct use in the current infrastructure as a drop-in fuel without an upgrading step. The presented work investigates the composition of an HTL bio-crude produced from lignocellulosic biomass at the pilot scale as well as the upgraded fuels obtained via catalytic hydrotreatment. Pentane solvent extraction is employed to fractionate the bio-crude and its hydrotreated counterpart into a light fuel extract and an asphaltene residue. The asphaltene fraction, which at room temperature is a solid material constituting 60 wt % of the bio-crude, is reduced upon hydrotreating to 34 wt%. The pentane extracts reveal a superior fuel quality in terms of higher heating value and composition. Detailed molecular and structural analysis via nuclear magnetic resonance (NMR), gas chromatography-mass spectrometry (GC-MS), and ultra high pressure liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS) revealed an aromatic and heteroatomatic structure of the asphaltene fraction. UHPLC-HRMS analysis indicated an average molecular weight ranging from 150 until 300 Da, which was affected by hydrotreating. A novel analytical strategy for UHPLC-HRMS, including weighted kernel density estimation, was developed. The superior quality of solvent extracted fuels suggests this could be a simple step in improving the capability of HTL derived bio-crudes in a refinery context. Additionally, the difficulty in hydrotreating the asphaltenes suggests that removal of this fraction via solvent extraction prior to the upgrading could be a viable option for improving the efficiency of this post-HTL treatment step.