Two organosolv lignins from different origins, namely, almond shells and maritime pine, were modified by using a nanoclay and nanosilicate. Prior to modification, they were activated via glyoxalation to enhance the reactivity of the lignins and thus ease the introduction of the nanoparticles into their structure. The lignins were characterized by several techniques (Fourier transformed infrared, high-performance size exclusion chromatography, 1H NMR, X-ray diffraction, and thermogravimetric analysis) before and after modification to elucidate the main chemical and structural changes. The reaction with glyoxal proved to increase the amount of hydroxyl groups and methylene bridges. This tendency was more pronounced, as the percentage of glyoxal was incremented. On the other side, the addition of the nanoclay and nanosilicate particles improved the thermal stability of the lignins compared to that of the original unmodified ones. This trend was more evident for the lignin derived from maritime pine, which displayed better results regarding the thermal stability, indicating a more effective combination of the nanoparticles in the lignin structure during the modification process.