In this paper we studied the effect of NaBO2 addition to a phase-separated alkali-free bioactive glass with a composition of 38.49 SiO2 • 36.07 CaO • 19.24 MgO • 5.61 P2O5 • 0.59 CaF2. Microscopy reveals binodal phase separation involving two Si-containing microphases with a droplet size of ∼200 μm, driven by the thermodynamic LLPS mechanism. The local environments and spatial distribution of silicate, phosphate, and fluoride ions in this phase-separated system were studied, using 29Si, 31P, 11B, 19F, 25Mg, and 23Na nuclear magnetic resonance (NMR) and infrared spectroscopy. The silicate units are dominantly of the metasilicate (Si2) type. The phosphate units exist mostly as orthophosphate (P0) while the borate is present in the form of pyroborate (B1). Multinuclear dipolar re-coupling experiments indicate that the minority components F, P, B and Na all occur within a common phase. Thus, atomic distribution scenarios involving the separation of these components into separate phases can be excluded. The 31P spin echo decay (SED) method was used along with Monte Carlo simulations to characterize the spatial distribution of the phosphate component. Based on the analysis, the phosphate component forms clusters of sizes 1-4 nm, which are embedded in an environment more dilute in phosphate, having a random distribution. While 19F SED results indicate that the fluoride ions do not form clusters and are close to randomly distributed, dipolar recoupling of 31P suggests a local environment resembling that of fluorapatite.