Flexible and crack-free bacterial cellulose (BC)–silica composite aerogels (CAs) are prepared through a sol–gel process followed by freeze drying, in which the BC matrix and silica gel skeleton form an interpenetrating network microstructure. The BC–silica CAs exhibit low density (0.02 g cm−3), high specific surface area (734.1 m2 g−1) and low thermal conductivity (0.031 W m−1 K−1), almost the same as pure silica aerogels. Due to the synergic effects of the BC matrix and silica gel skeleton, the obtained CAs show excellent robustness and flexibility which overcome the inherent fragility of traditional inorganic aerogels. Furthermore, the dried CAs can withstand a huge capillary force and keep their integrity and flexibility even upon being immersed in a liquid phase again. Hence, the CAs can be functionalized conveniently in a liquid phase to extend their applications. The hydrophobization modified CAs have potential to be used as adsorbents for water purification and show excellent oil absorption capability on the surface of water, and can be removed from water conveniently.