Chemical modification of lignocellulosic fillers is a hydrophobization process that has been used for years in the production of wood-polymer composites (WPCs). However, finding new, more effective modifiers is still a big challenge and remains the subject of much research. This study involved the chemical modification of wood with the use of newly designed ammonium and imidazolium ionic liquids containing reactive functional groups. The effectiveness of the modification was confirmed using FTIR and XRD techniques. The effect of modification of wood on the supermolecular structure and morphology of wood-polymer composites was investigated by X-ray diffraction, hot stage optical microscopy and differential scanning calorimetry. A significant influence of the modifier structure on the shaping of polymorphic varieties of the polymer matrix was demonstrated. The chemical modification also had significant effect on the nucleating properties of the wood fillers, which was confirmed by the determined crystallization parameters (crystallization half-time, crystallization temperature, crystal conversion). Moreover, the formation of a transcrystalline PP layer was noticed, which showed a large variation depending on the structure of the used ionic liquid. The obtained results correlated very well with the results of mechanical tests. It has been shown that it is possible to precisely design an ionic liquid containing a reactive functional group capable of interacting with hydroxyl groups of cellulose molecules. Moreover, the possibility of functionalizing the lignocellulosic material with innovative ionic liquids without the need to use organic solvents has not been demonstrated so far.Graphic abstract