The long-term fate of nanomaterials in biological environment represents a critical matter, which determines environmental effects and potential risks for human health. Predicting these risks requires understanding of nanoparticle transformations, persistence, and degradation, some issues somehow ignored so far. Safe by design, inorganic nanostructures are being envisioned for therapy, yet fundamental principles of their processing in biological systems, change in physical properties, and in situ degradability have not been thoroughly assessed. Here we report the longitudinal visualization of iron oxide nanocube transformations inflicted by the intracellular-like environment. Structural degradation of individual nanocubes with two different surface coatings (amphiphilic polymer shell and polyethylene glycol ligand molecules) was monitored at the atomic scale with aberration-corrected high-resolution transmission electron microscopy. Our results suggest that the polymer coating controls surface reactivity and that availability and access of chelating agents to the crystal surface govern the degradation rate. This in situ study of single nanocube degradation was compared to intracellular transformations observed in mice over 14 days after intravenous injection, revealing the role of nanoparticle clustering, intracellular sorting within degradation compartments, and iron transfer and recycling into ferritin storage proteins. Our approach reduces the gap between in situ nanoscale observations in mimicking biological environments and in vivo real tracking of nanoparticle fate.