Supercritical drying is widely considered as the gold standard to produce aerogels that preserve the microstructure of the gels, but we have found this is not always the case. Chitosan aerogel, one of the emerging biopolymer aerogels, was prepared by chemical cross-linking gelation, followed by solvent exchange with methanol and supercritical drying using CO2. Small-angle X-ray scattering analysis shows that the structure of the wet gel, which consists of Gaussian chains of individual molecular strands, converts into a nanofibrous network during CO2 processing. In situ observation reveals a drastic shrinkage of the gel in CO2, demonstrating that physical coagulation caused by the low affinity between chitosan and CO2 is the main structure-forming step. These results challenge the common perception of supercritical drying: it is no longer an inactive drying method, but rather an active nanostructure forming a tool to produce porous biopolymer materials with tailored structure and properties.