Ca- and P-based bioactive glasses are excellent candidates for design and manufacture of biomaterials. Understanding the structure and physico-chemical-thermal behaviour of bioactive glasses is a fundamental step towards the design of a new generation of biocompatible materials. In this study, the structure of SiO2-CaO-Na2O glasses and its derivatives, obtained by substituting Na2O with P2O5 and prepared by melt-quench technique, was studied with neutron and electron diffraction techniques combined with thermal analysis, high-resolution electron microscopy and X-ray photoelectron spectroscopy. Neutron and electron diffraction data were analysed with reverse Monte Carlo simulation and pair distribution function analysis, respectively. Bioactivity of P2O5 substituted glasses was also investigated and proven in vitro using simulated body fluid. Based on the structural analysis, it was found that Si and P atoms are in well-defined tetrahedral units with a bond distance of 1.60 angstrom for both Si-O and P-O bonds, although P exhibits a higher average coordination number than Si. With increasing phosphate content, tendentious changes in the glass behaviour were observed. Linear increase in T-g, supported by the changes in the average coordination numbers of Si and P, indicates strengthening of network structure with increasing P content and formation of P-O-Ca atomic linkages, which lead to Ca-P-rich atomic environments in the silicate network. These Ca-P-rich environments trap volatile elements and thus decrease the total weight loss during heating at higher P concentrations. In the case of the highest investigated P2O5 content (5 mol%), nanoscale structural inhomogeneity and the formation of Ca-P-rich clusters were also revealed by electron diffraction and atomic resolution imaging. This type of Ca-(Na)-P clustering has a key role in the behaviour of phosphate-substituted silicate glasses under physiological conditions.