Using metal coordination to assemble carbon nanodots (CND) into clusters can enhance their photophysical properties for applications in sensing and biomedicine. Water-soluble clusters of CNDs are prepared by one-step microwave synthesis starting from ethylenediaminetetraacetic acid, ethylenediamine and MnCl2·4H2O as precursors. Transmission electron microscopy and powder X-Ray diffraction techniques indicate that the resulting clusters form spherical particles of 150 nm constituted by amorphous CNDs joined together with Mn ions in a laminar crystalline structure. The nanomaterial assemblies show remarkable fluorescence quantum yields (0.17–0.20) and magnetic resonance imaging capability (r1 = 2.3-3.8 mM–1.s–1). In addition, they can be stabilized in aqueous solutions by phosphate ligands, providing a promising dual imaging platform for use in biological systems.