Abstract Soils contain an abundance of nano-size particles. Because of their tendency to aggregate and associate with organic colloids, however, soil nanoparticles are difficult to obtain and characterize. Here we report on a simple and rapid method of extracting mesoporous nanomaterials from the clay fraction of an Andisol with narrow size distribution. The clay and nanoclay were characterized by elemental analysis, pyrolysis GC/MS, electron and atomic force microscopy, infrared spectroscopy, and electrophoresis. The nanoclay dominantly consists of hollow allophane spherules forming globular aggregates of about 100 nm in diameter. The nanoclay contains more organic matter (carbon and nitrogen) with a larger proportion of polysaccharides and nitrogen containing compounds, and has a lower isoelectric point, than the clay. Treatment with hydrogen peroxide causes a large decrease in the organic matter contents of both nanoclay and clay. The aggregates of allophane nanoparticles retain a significant amount (~ 12%) of carbon against intensive peroxide treatment. Thus, besides playing an important role in carbon stabilization, these naturally occurring nanomaterials are potentially useful for developing a low-cost carbon sequestration technology.