Nanogold is widely used in many areas of physics and chemistry due to its environment-sensitive plasmon resonance absorption. The immobilization of gold nanoparticles in highly porous silica aerogel offers an attractive alternative to liquid gold solutions as they show a mechanically stable structure, are permeable to gases, and can even be used at elevated temperatures. We have found that the commercially available citrate-stabilized 10 nm gold nanoparticles may suffer from aggregation prior to or under the base-catalyzed gelation process of tetramethoxy silane. In the wet gels, Au particles increased in size, changed shape, and demonstrated the loss of plasmon resonance absorption, due to the formation of larger aggregates. We have studied a range of water-miscible organic solvents, stabilizing agents, and the gelation conditions to minimize changes from occurring in the aerogel setting and the supercritical drying process. It has been found that atmospheric carbon dioxide has a significant effect on aggregation, and it cannot be entirely excluded under normal synthetic conditions. Methanol resulted in an increase in the particle size only, while dimethyl sulfoxide, dimethylformamide, and urea changed the shape of nanoparticles to rod-like shapes, and diols led to an increase in both size and shape. However, using the polymeric stabilizer poly(vinyl pyrrolidone) efficiently prevented the aggregation of the particles, even in the presence of high concentrations of carbon dioxide, and allowed the production of nanoAu containing silica aerogels in a single step, without the modification of technology.