The interactions that occur between an amorphous silicon nitride (Si3N4) nanofiller and an epoxy matrix are examined, as revealed by rheological changes in a diglycidyl ether of bisphenol-A (DGEBA)-based epoxy resin prior to curing and thermal analysis, scanning electron microscopy, and dielectric spectroscopy of the resulting amine-cured systems. The results show that isothermally heating the as-received Si3N4 in DGEBA at 100 °C leads to increases in the viscosity of the mixture. Analysis of rheological data obtained from unfilled, as-received Si3N4-filled, and calcined Si3N4-filled epoxy systems leads us to interpret this increase in viscosity as arising from reactions between epoxide groups of the DGEBA and nanoparticle surface groups, notably involving surface amines, which are stimulated by the elevated temperature. The extent of this filler/resin reaction depends on the material processing protocol used, particularly prior calcination of the Si3N4 and the temperature and duration of nanoparticle/DGEBA mixing. Glass transition temperature data show that cured samples prepared using different methods have significantly different glass transition temperatures, which is a consequence of the epoxide/amine stoichiometric imbalances that result from prior reactions between the Si3N4 and the DGEBA. Consistent behavior was observed in the dielectric response. These results demonstrate that ultimate macroscopic properties of Si3N4/epoxy nanocomposites are critically affected by details of the processing protocol. Furthermore, we infer that, by using controlled prior calcination of the Si3N4, it is may be possible to vary the initial surface chemistry of the nanoparticles so as to adjust their reactivity with epoxy-containing moieties. Here, this is exemplified using only two somewhat extreme thermal treatments and a bifunctional DGEBA-type compound but, we suggest, that the concept may be extended to many other mono- and polyfunctional epoxy-containing compounds in order to generate a wide range of different grafted nanoparticle systems. This strategy may provide a versatile means of adjusting the surface chemistry of inorganic nitride nanoparticles, in order to tailor their surface chemistry and thereby modify resulting nanocomposite properties.