There are very few methods to investigate how nanoparticles (NPs) are taken up and processed by cells in the organism in the short and long terms. We propose a nanomagnetism approach, in combination with electron microscopy, to document the magnetic outcome of iron oxide-based P904 NPs injected intravenously into mice. The NP superparamagnetic properties are shown to be modified by cell internalization, due to magnetic interactions between NPs sequestered within intracellular organelles. These modifications of magnetic behaviour are observed in vivo after NP uptake by resident macrophages in spleen and liver or by inflammatory macrophages in adipose tissue as well as in vitro in monocyte-derived macrophages. The dynamical magnetic response of cell-internalized NPs is theoretically and experimentally evidenced as a global signature of their local organization in the intracellular compartments. The clustering of NPs and their magnetism become dependent on the targeted organ, on the dose administrated and on the time elapsed since their injection. Nanomagnetism probes the intracellular clustering of iron-oxide NPs and sheds light on the impact of cellular metabolism on their magnetic responsivity.