In the pursuit of optimized magnetic nanostructures for diagnostic and therapeutic applications, the role of nanoparticle architecture has been poorly investigated. In this study, we demonstrate that the internal collective organization of multi-core iron oxide nanoparticles can modulate their magnetic properties in such a way as to critically enhance their hyperthermic efficiency and their MRI T1 and T2 contrast effect. Multi-core nanoparticles composed of maghemite cores were synthesized through a polyol approach, and subsequent electrostatic colloidal sorting was used to fractionate the suspensions by size and hence magnetic properties. We obtained stable suspensions of citrate-stabilized nanostructures ranging from single-core 10 nm nanoparticles to multi-core magnetically cooperative 30 nm nanoparticles. Three-dimensional oriented attachment of primary cores results in enhanced magnetic susceptibility and decreased surface disorder compared to individual cores, while preserving a superparamagnetic-like behavior of the multi-core structures and potentiating thermal losses. Exchange coupling in the multi-core nanoparticles modifies the dynamics of the magnetic moment in such a way that both the longitudinal and transverse NMR relaxivities are also enhanced. Long-term MRI detection of tumor cells and their efficient destruction by magnetic hyperthermia can be achieved thanks to a facile and nontoxic cell uptake of these iron oxide nanostructures. This study proves for the first time that cooperative magnetic behavior within highly crystalline iron oxide superparamagnetic multi-core nanoparticles can improve simultaneously therapeutic and diagnosis effectiveness over existing nanostructures, while preserving biocompatibility.