In this work, design and physiochemical characterization of a biocompatible nanoplatform with integrated photoluminescence and magnetic properties were reported. The potential in vivo toxicity was assessed by exploring the biodistribution of nanoparticles using synchrotron X-ray fluorescence (SXRF) imaging in the zebrafish embryos as a biological model. Their synthesis is accessible through combining magnetic iron oxide nanoparticles with Ce 3+ -and Tb 3+ -doped GdOF luminophore and concurrent capping in situ with chitosan biopolymer. The Fe 3 O 4 @SiO 2 / GdOF:xCe 3+ ,yTb 3+ nanoparticles manifested near superparamagnetic behavior at 300 K, displaying green emission lines, arising from the characteristic 5 D 4 → 7 F J transitions (J = 6−0) of Tb 3+ ion. The limited permeability of the chorion membrane is a critical factor in toxicity screening, a potential approach to remove the chorion and expose the chorion-off zebrafish embryos to nanoscale materials. Accordingly, multifunctional nanoparticles exhibited no acute toxicity to the with-chorion and chorion-off zebrafish embryos up to 100 mg L −1 exposure concentration, suggesting remarkable in vivo biocompatibility. By assessing the nanobio interaction via deep-tissue SXRF imaging, it was visualized that the distribution of Gd and Fe elements had occurred with a roughly constant relative ratio in the whole body of early-stage embryos. However, the elements mapping data revealed a predominant localization of Gd and Fe in the gastrointestinal tract, manifesting bioaccumulation of magneto-luminescent nanoparticles as an integrated nanoplatform in the respective region. This result demonstrated that the particles' uptake by embryos were mostly through oral exposure rather than the dermal pathway, offering a new route to oral administration of nanoparticles for future biological and environmental applications.