The use of magnetic nanostructures as theranostic agents is a multiplex task as physiochemical and biochemical properties including excellent magneto-responsive properties, low toxicity, colloidal stability and facile surface engineering capability are all required. Nonetheless, much progress has been made in recent years synthesis of “all-in-one” MNPs remain unambiguously challenging. Towards this direction, in this study is presented a facile incorporation of a soft magnetic phase (MnFe2O4 NPs) with a hard phase (CoFe2O4 NPs) in the presence of the biocompatible polymer sodium dodecyl sulfate (SDS), into spherical and compact bi-magnetic nanoclusters (NCs) with modulated magnetic properties that critically enhance hyperthermic efficiency and MRI contrast effect. Hydrophobic MnFe2O4 and CoFe2O4 NPs coated with oleylamine of the same size (9 nm) were used as primary building units for the formation of the bi-magnetic NCs through a microemulsion approach where a set of experiments were conducted to identify the optimal concentration of SDS (19.5 mM) for the cluster formation. Additionally, homo-magnetic NCs of MnFe2O4 NPs and CoFe2O4 NPs, respectively were synthesized for comparative studies. The presence of distinct magnetic phases within the bi-magnetic NCs resulting in synergistic behavior, where the soft phase offers moderate coercivity Hc and the hard one high magnetization Ms. Increased specific loss power (SLP) value was obtained for the bi-magnetic system (525 W/g) when compared with the homo-magnetic NCs (104 W/g for MnNCs and 223 W/g for CoNCs) under field conditions of 25 kA/m and 765 kHz. Relaxivities (r2) of the bi-magnetic NCs were also higher (81.8 mM−1 s−1) than those of the homo-magnetic NCs (47.4 mM−1 s−1 for MnNCs and 3.1 mM−1 s−1 for CoNCs), while the high r2/r1 value renders the system suitable for T2-weighted MRI imaging