The continuous trend towards enhancing the bio-based content of polyurethanes in parallel with balancing their properties for optimized chemical, physical and mechanical properties has lead to the exploration of various alternative components of bio-based diisocyanates, polyols and their combination. In this work, the role of a semi bio-based aliphatic diisocyanate polymer synthesized from hexamethylene diisocyanate (HDI), poly(ethylene glycol) and palmitic acid containing 32 % bio-based carbon content was investigated as a reactive diluent and crosslinker in combination with the pentamethylene diisocyanate (PDI) containing 68% bio-based carbon content, and a reference petrol-based hexamethylene diisocyanate (HDI). The diisocyanate mixtures were consequently crosslinked with a selected polyester polyol for making fast air-drying 2K solvent-free coating formulations, which were evaluated on mechanical and thermophysical properties. The addition of the synthesized aliphatic diisocyanate in combination with both PDI or HDI resulted in homogeneous mixtures up to 1:1 concentrations, with a progressive reduction in viscosity and possible formation of smooth coatings on wood. Therefore, the aliphatic diisocyanate functions as a levelling agent, enhancing flow and gloss levels of the coating, while introducing hydrophobicity through an increase in water contact angles. The mechanical properties of crosslinked polyurethanes demonstrated higher flexibility and ductility, owing to the molecular configuration of the aliphatic diisocyanate, resulting in a reduced hardness and better resistance against scratching or abrasive wear for balanced concentrations of crosslinkers. The performance was confirmed through FTIR spectroscopy, indicating the higher crosslinking densities and presence of hydrophobic moieties at the surface. The curing reactions were confirmed by DSC and DMA measurements, confirming the progressive shift in glass transition temperatures, loss modulus and dampening peak depending on aliphatic diisocyanate concentrations, confirming its role as a plasticizer.