Silica polymerization from its soluble monomers is fundamental to many chemical processes. Although industrial methods require harsh conditions and concentrated precursors, biological silica precipitation occurs under ambient conditions from dilute solutions. The hallmark of biosilica is the presence of amine-rich organic macromolecules, but their functional role remains elusive. Here, we show a pH-dependent stimulatory effect of such polyamines on silica polymerization. Notably, this process is decoupled from the saturation degree, allowing the synthesis of polymer−silica hybrid products with controlled network morphologies from undersaturated solutions. The data suggest a two-step phase separation process. First, an associative liquid−liquid phase separation forms a micrometer-size dense phase. Second, silica undergoes a liquid-to-solid transition in the supersaturated condensates to form a bicontinuous silica structure. This study can inspire "soft chemistry" routes to design organic−inorganic nanomaterials with regulatory principles optimized by evolution.