Multifunctional nano-heterostructures (NHSs) with controlled morphology are cardinal in many applications, but the understanding of the nanoscale colloidal chemistry is yet to be fulfilled. The stability of the involved crystalline phases in different solvents at mid- and high-temperatures and reaction kinetics considerably affect the nucleation and growth of the materials and their final architecture. The formation mechanism of manganese ferrite-based core-shell NHSs is herein investigated. The effects of the core size (8, 10, and 11 nm), the shell nature (cobalt ferrite and spinel iron oxide) and the polarity of the solvent (toluene and octanol) on the dissolution phenomena of manganese ferrite are also studied. Noteworthily, the combined use of bulk (powder X-ray diffraction, 57Fe Mössbauer spectroscopy, and DC magnetometry) and nanoscale techniques (HRTEM and STEM-EDX) provides new insights into the manganese ferrite dissolution phenomena, the colloidal stability in an organic environment, and the critical size below which dissolution is complete. Moreover, the dissolved manganese and iron ions react further, leading to an inverted core-shell in the mother liquor solution, paving the way to novel synthetic pathways in nanocrystal design. The MnFe2O4@CoFe2O4 core-shell heterostructures were also employed as heat mediators, exploiting the magnetic coupling between a hard (CoFe2O4) and a soft phase (MnFe2O4).