Here we show that it’s possible to produce different magnetic core-multiple shells heterostructures from monodispersed iron oxide spherical magnetic seeds by finely controlling the amount of a manganese precursor and using in a smart and simple way a cation exchange synthetic approach. In particular, by increasing the amount of precursor we were able to produce nanostructures ranging from Fe3O4/Mn-ferrite core/single shell nanospheres to larger, flower-like Fe3O4/Mn-ferrite/Mn3O4 core-double shell nanoparticles. We first demonstrate how the formation of the initial thin manganese-ferrite shell determines a dramatic reduction of the superficial disorder in the starting iron oxide, bringing to nanomagnets with lower hardness. Then, the growth of the second and most external manganese oxide shell causes the magnetical hardening of the heterostructures, while its magnetic exchange coupling with the rest of the heterostructure can be antiferromagentic or ferromagnetic, depending on the strength of the applied external magnetic field. This response is similar to that of an iron oxide-manganese oxide core-shell system but differs from what observed in multiple-shell heterostructures. Finally, we report as the most external shell becomes magnetically irrelevant above the ferrimagnetic-paramagnetic transition of the manganese oxide and the resulting magnetic behavior of the flower-like structures is then studied in-depth.