This work presents a rapid and facile way to access the cell wall of wood with magnetic nanoparticles (NPs), providing insights into a method of wood modification to prepare hybrid bio-based functional materials. Diffusion-driven infiltration into Scots pine (Pinus sylvestris L.) sapwood was achieved using colloidal Fe₃O₄ nanoparticles. Optical microscopy, scanning electron microscopy/energy-dispersive X-ray spectroscopy, transmission electron microscopy, and X-ray powder diffraction analyses were used to detect and assess the accessibility of the cell wall to Fe₃O₄. The structural changes, filling of tracheids (cell lumina), and NP infiltration depth were further evaluated by performing X-ray microcomputed tomography analysis. Fourier transform infrared spectroscopy was used to assess the chemical changes in Scots pine induced by the interaction of the wood with the solvent. The thermal stability of Fe₃O₄-modified wood was studied by thermogravimetric analysis. Successful infiltration of the Fe₃O₄ NPs was confirmed by measuring the magnetic properties of cross-sectioned layers of the modified wood. The results indicate the feasibility of creating multiple functionalities that may lead to many future applications, including structural nanomaterials with desirable thermal properties, magnetic devices, and sensors.