In this study, we have developed novel biomimetic silica composite aerogels and cryogels for the first time, drawing inspiration from the natural diatom’s silicification process. Our biomimetic approach involved the modification of tyrosinase-mediated oxidized silk fibroin (SFO) surfaces with polyethyleneimine (PEI). This modification introduced ample amine groups onto the SF polymer, which catalyzed the silicification of the SFO-PEI gel surface with silicic acid. This process emulates the catalytic function of long-chain polyamines and silaffin proteins found in diatoms, resulting in a silica network structure on the primary SFO-PEI network gel’s surface. The SFO-PEI gel matrix played a dual role in this process: (1) It provided numerous amine functional groups that directly catalyzed the silicification of silicic acid on the porous structure’s exterior surface, without encapsulating the created silica network in the gel. (2) It served as a flexible mechanical support facilitating the creation of the silica network. As a result, the final ceramic composite exhibits a mechanically flexible nature (e.g., cyclic compressibility up to 80% strain), distinguishing it from conventional composite aerogels. By mimicking the diatom’s silicification process, we were able to simplify the development of silica-polymer composite aerogels. It eliminates the need for surfactants, multi-step procedures involving solvent exchange, and gel washing. Instead, the reaction occurs under mild conditions, streamlining the composite aerogels fabrication process.