Oxyhalide-containing silicate glasses have been receiving increasing attention in recent years due to their extensive medical and dental applications. This manuscript reports the first detailed structural investigation using MD simulations in the context of chloride- and mixed-fluoride/chloride-containing phospho-silicate bioactive glasses. It is shown that adding fluoride, chloride, and mixed fluoride and chloride has not altered the Q n silicate distribution and phosphorus speciation significantly in all of the glasses investigated. The Q2 silicon species is the predominant species with smaller and nearly equal proportions of Q1 and Q3 species, whereas phosphorus is largely present as orthophosphate Q0 units. No Si-F/Cl and P-F/Cl bonds have been observed at room temperature. Both F and Cl anions are present as F-Ca(n) and Cl-Ca(n). MD simulations also indicate opposite effects of fluoride and chloride on the crystallization ability of the glasses. The environment of Cl in chloride-containing glass series is quite different from the chlorapatite and CaCl2 crystals, and a significant structural reorganization is required to observe the appearance of the crystal nuclei. Instead, the environment of fluoride ions in the glasses is quite similar to that present in the FAP and CaF2 crystals and thus F-containing glasses manifest a high crystallization tendency. Moreover, in the mixed-fluoride/chloride-containing glasses, fluorine tends to surround phosphate, whereas chloride moves toward the silicate network. Finally, it was observed that a good correlation exists between the glass transition temperature and the overall strength of the glass network quantified by the Fnet factor.