Heating magnetic nanoparticles (MNPs) with AC (Alternating Current) magnetic fields has received significant attention in recent years, particularly for biomedical uses. However, most studies focus on characterizing the heat release, overlooking the fact that the MNPs in the viscous cell environment constitute a dynamic magnetic colloid whose configuration may evolve over time, particularly if a driving force as the AC field is applied. Aiming to shed light on this matter, in this workthe dynamics of the colloid structure during hyperthermia experiments are studied. By combining various experimental and theoretical tools, it is concluded that the AC field may drive the formation of aligned structures, and the impact that such structures may have on the associated heating is assessed. Remarkably, the results show that those field‐driven structures are highly unstable for small particle sizes, rapidly disassembling upon field removal. Moreover, an analogous behavior in vitro is found, with the AC magnetic field also promoting a reversible alignment of vesicles containing the MNPs within the cells. The results suggest that the observed alignment, both of MNPs and intracellular vesicles, may be a common phenomenon in usual hyperthermia experiments, but unnoticed because of the intrinsic unstable nature of the aligned structures.