Quantitative studies of the long-term fate of iron oxide nanoparticles inside cells, a prerequisite for regenerative medicine applications, are hampered by the lack of suitable biological tissue models and analytical methods. Here, we propose stem-cell spheroids as a tissue model to track intracellular magnetic nanoparticle transformations during long-term tissue maturation. We show that global spheroid magnetism can serve as a fingerprint of the degradation process, and we evidence a near-complete nanoparticle degradation over a month of tissue maturation, as confirmed by electron microscopy. Remarkably, the same massive degradation was measured at the endosome level by single-endosome nanomagnetophoretic tracking in cell-free endosomal ex...