The process of magnetic nanoparticle heating releases enormous amounts of thermal energy. Through typical calorimetric analyses, the total thermal energy released can be easily quantified; however, knowledge of nanoscale temperature is necessary. Herein, a novel method of nanoscale thermometry by analyzing intra-particle diffusion in core–shell nanoparticles is proposed. Heating the iron cores with an alternating magnetic field in a saline suspension encourages the diffusion of sodium ions into the silica shells of the particles, which is modeled numerically; however, experimental measurements are needed in order to provide accurate diffusivity estimations. After determining the diffusion characteristics from X-ray photoelectron spectroscopy) depth profiling of silica films, energy dispersive analysis with high-resolution transmission electron microscopy measures the sodium ion gradient within single particles before and after heating. When compared directly to the numerical simulations, the results indicate that the temperature gradient between particles and saline suspension reaches significantly higher temperatures than the macro-scale temperature of the solution. By accurately knowing the thermal gradient between nanoparticles and the surrounding medium, nanoparticles can be engineered to limit surface resistances as much as possible and promote high rates of thermal energy transfer.