This research aimed to prove the existing natural transition of Metal Coordination Anthocyanin complex (MAC) from the freeze-dried of Java plum (Syzygium cumini) fruit and its role as free radical scavenging. The Liquid Chromatography-Mass Spectrometry (LCMS) analysis showed the presence of anthocyanin in the fruit, while transition metals of Fe, Cu, and Ni were also found as detected by X-Ray Fluorescence (XRF). The Fourier Transform Infrared Spectroscopy (FTIR) spectra revealed the interaction of organic functional groups with transition metals. These facts were supported by X-Ray Powder Diffraction (XRD) and polarizing microscope images which displayed both amorphous and crystallite microstructures related to organic and bioinorganic content in the fruit. The analysis of complex compound indicated the transition metal as coordinator atom and a cyanidin acts as a chelator among anthocyanins existing in the fruit. The paramagnetic property of MAC in the fruit as a free radical scavenger was demonstrated by the reduction of 1, 1-diphenyl-2-picrylhydrazyl (DPPH) radical intensity in the Electron Spin Resonance (ESR) spectrum. These findings suggested that S.cumini fruit contains naturally existing MAC.