In the view of designing functional nanoparticles, the encapsulation of 1,4,7,10-tetraazacyclododecane (cyclen) within silica nanoparticles using the Stober process was studied. In the presence of cyclen and tetraethoxysilane (TEOS), silica particles exhibiting an unusual core-shell structure were obtained. On then basis of TEM, DLS, and NMR data, we suggest that the particle core is constituted of hybrid primary nanoparticles resulting from cyclen-silica interactions, whereas the shell formation results from further condensation of unreacted silica precursors. Control experiments performed with the zinc-cyclen complex and ammonia addition suggest that cyclen-TEOS interactions arise from the activation of the silicon alkoxide hydrolysis with the polyazamacrocycle amine groups. These data are discussed in the context of silica biomineralization mechanisms, where polyamine/silica interactions have been shown to play a major role. Moreover, the possibility to control the size and the structure of these nanoparticles makes them promising materials for pharmaceutical applications.