Emulsion polymer isocyanate (EPI) and urea-formaldehyde (UF) were selected as typical resin systems to investigate the microstructure of wood–adhesive interphases by fluorescence microscopy (FM) and confocal laser scanning microscopy (CLSM). Further, a quantitative micromechanical analysis of the interphases was conducted using nanoindentation. The FM results showed that the UF resin could penetrate the wood to a greater extent than the EPI resin, and that the average penetration depth for these two resin systems was higher in the case of latewood. CLSM allowed visualization of the resin distribution with contrasting colors, showing that the EPI resin could not penetrate the cell wall, whereas UF resin could enter the cell walls. The micromechanical properties of the cell walls were almost unaffected by EPI penetration but were significantly affected by UF penetration, especially in the first cell wall from the glueline. This further confirmed that only cell walls with resin penetration can improve the mechanical properties of the interphase regions.