Borosilicate glasses for nuclear waste applications are limited in waste loading by the precipitation of watersoluble molybdates. In order to increase storage efficiency, new compositions are sought out that trap molybdenum in a water-durable CaMoO4 crystalline phase. Factors affecting CaMoO$_4$ combination and glass-inglass phase separation in calcium borosilicate systems as a function of changing [MoO$_3$] and [B$_2$O$_3$] are examined in this study in order to understand how competition for charge balancers affects phase separation. It further examines the influence of radiation damage on structural modifications using 0.77 to 1.34 GGy of 2.5 MeV electron radiation that replicates inelastic collisions predicted to occur over long-term storage. The resulting microstructure of separated phases and the defect structure were analyzed using electron microscopy, XRD, Raman and EPR spectroscopy prior to and post irradiation. Synthesized calcium borosilicates are observed to form an unusual heterogeneous microstructure composed of three embedded amorphous phases with a solubility limit ~2.5 mol% MoO$_3$. Increasing [B$_2$O$_3$] increased the areas of immiscibility and order of (MoO$_4$)$^{2−}$anions, while increasing [MoO$_3$] increased both the phase separation and crystallization temperature resulting in phases closer to metastable equilibrium, and initiated clustered crystallization for [MoO$_3$]> 2.5 mol%. β-irradiation was found to have favorable properties in amorphous systems by creating structural disorder and defect assisted ion migration that thus prevented crystallization. It also increased reticulation in the borosilicate network through 6-membered boroxyl ring and Si ring cleavage to form smaller rings and isolated units. This occurred alongside an increased reduction of Mo$^{6+}$with dose that can be correlated to molybdenum solubility. In compositions with existing CaMoO$_4$ crystallites, radiation caused a scattering effect, though the crystal content remained unchanged. Therefore β-irradiation can preferentially prevent crystallization in calcium borosilicates for [MoO$_3$] < 2.5 mol%, but has a smaller impact on systems with existing CaMoO$_4$ crystallites.