Magnetite and maghemite multi-core nanoflowers (NFs) synthesized using the modified polyol-mediated routes are to date among the most effective nano-heaters in magnetic hyperthermia (MHT). Recently, magnetite NFs have also shown high photothermal (PT) performances in the most desired second near infra-red (NIR-II) biological window making them attractive in the field of nanoparticle-activated thermal therapies. However, what makes 2 magnetic NFs efficient heating agents in both modalities still remain an open question. In this work, we investigate the role of many parameters of the polyol synthesis on the final NFs size, shape, chemical composition, number of cores and crystallinity. These nanofeatures are later correlated to the magnetic, optical and electronic properties of the NFs as well as their collective macroscopic thermal properties in MHT and PT to find relationships between their structure, properties and function. We evidence the critical role of iron(III) and heating ramps on the elaboration of well-defined NFs with high number of multi-cores. While MHT efficiency is found to be proportional to the average number of magnetic cores within the assemblies, the optical responses of the NFs and their collective photothermal properties depend directly on the mean volume of the NFs (as supported by optical cross sections numerical simulations) and strongly on the structural disorder in the NFs, rather than the stoichiometry. The concentration of defects in the nanostructures, evaluated by photoluminescence and Urbach energy (EU), evidences a switch in the optical behavior for a limit value of EU = 0.4 eV where a discontinuous transition from high to poor PT efficiency is also observed.