The preparation of silica-containing organic–inorganic hybrid materials composed of kraft lignin, alkoxysilanes, and organic linkers was investigated. 3-Glycidyloxypropyltrimethoxysilane, 3-(triethoxysilyl)propylisocyanate (IPTES), and bis(trimethoxysilyl)hexane were selected as the most promising linkers. The best materials obtained showed improved mechanical and thermal properties compared with lignin itself. The reaction of the hydroxyl groups with IPTES and the sol–gel reaction between the organic linker molecules were studied by attenuated total reflectance FTIR and solid-state 29Si magic-angle spinning NMR spectroscopy. The homogeneous composition was demonstrated by electron microscopy and energy-dispersive X-ray spectroscopy mapping. The mechanical properties were investigated by microindentation and dynamic mechanical thermal analysis.