Nowadays, the protection of wood is becoming more important with the increasing demand for durable wood, in addition to its limited accessibility. One possible way to increase the durability is the use of nanoparticles, which can be effective even with a low intake of active ingredients. However, avoiding their leaching is a challenge. A possible solution to leaching is the use of silica aerogel as a fixative. This study investigated the use of mesoporous silica aerogel against the leaching of different nanoparticles under laboratory conditions. Tests were performed involving beech (Fagus sylvatica) and Scots pine (Pinus sylvestris) sapwood, using Trametes versicolor as a white rot and Coniophora puteana as a brown rot fungus. The results show that the subsequent treatment of the wood with mesoporous silica aerogel effectively fixed the nanoparticles in wood. The durability of the samples without aerogel significantly decreased as a result of leaching, whereas the resistance of the samples treated with aerogel decreased only slightly. However, the silica aerogel modification itself caused the leaching of silver nanoparticles, which is a limitation in the use of this method for the fixation of nanoparticles.