Understanding the interactions of nanomaterials with complex tumour models is essential for advancing their use in nanomedicine. Calcium fluoride nanoparticles doped with neodymium and yttrium (CaF₂:Nd3+, Y3+) exhibit promising properties for biomedical applications, particularly for optical sensing and tagging. This study investigates their interaction with 3D cell spheroids derived from breast cancer (MCF-7) and brain cancer (U-87 MG) cell lines as tumour models. Specific protocols have been developed in Total-reflection X-Ray Fluorescence (TXRF) to evaluate nanoparticles’ internalisation and diffusion within spheroids by quantifying the concentrations of Ca, Nd, and Y taken up by the cells. Minimal background interference enabled precise multi-element detection in low-volume biological samples, yielding very low detection limits and minimal uncertainties. The study demonstrates the effectiveness of TXRF for quantifying rare-earth-doped nanoparticles in 3D cancer models and reveals that, although both cell lines permit nanoparticle diffusion into cells, higher accumulation is observed in glioblastoma cell spheroids. A Weibull diffusion model was applied to help understand the observed internalisation kinetics of nanoparticles into U-87 MG and MCF-7 spheroids. The relevant differences suggest cell-line-dependent uptake behaviour, potentially influenced by differences in cellular architecture, the porosity of the generated spheroid, and its intercellular 3D microstructure. These findings highlight the importance of tumour-specific interactions in the investigation of nanoparticle systems for targeted cancer diagnostics and therapeutics.