Understanding how calcium interacts with silica sources and influences their polycondensation in aqueous solutions is of central importance for the development of more effective biomaterials by sol-gel approaches. For this purpose, the atomic-scale evolutions of a calcium-containing precursor solution corresponding to a typical sol-gel bioactive glass and of a corresponding Ca-free solution were compared using reactive molecular dynamics simulations. The simulations highlight a significantly faster rate of condensation when calcium is present in the initial solution, resulting in the formation of large and ramified silica clusters within 5 ns, which are absent in the Ca-free system. This different behavior has been analyzed and interpreted in terms of the Ca-induced nanosegregation in calcium-rich and silica-rich regions, which promotes the condensation reactions within the latter. By identifying a possible mechanism behind the limited incorporation of calcium in the silica nanoclusters formed in the early stages of the sol-gel process, these results could guide further studies aimed at identifying favorable experimental conditions to enhance initial calcium incorporation and thus produce sol-gel biomaterials with improved properties.