Organic compounds isolated from diatoms contain long-chain polyamines with a propylamine backbone and variable methylation levels and chain lengths. These long-chain polyamines are thought to be one of the important classes of molecules that are responsible for the formation of the hierarchically structured silica-based cell walls of diatoms. Here we describe a synthetic route based on solid-phase peptide synthesis from which well-defined long-chain polyamines with different chain lengths, methylation patterns, and subunits can be obtained. Quantitative silica precipitation experiments together with structural information about the precipitated silica structures gained by scanning and transmission electron microscopy revealed a distinct dependence of the amount, size, and form of the silica precipitates on the molecular structure of the polyamine. Moreover, the influence of the phosphate concentration was elucidated, revealing the importance of divalent anions for the precipitation procedure. We were able to derive further insights into the precipitation properties of long-chain polyamines as functions of their hydrophobicity, protonation state, and phosphate concentration, which may pave the way for better control of the formation of nanostructured silica under ambient conditions.