Simultaneously acquired microanalytical X-ray and electron energy loss signals are obtained from a bimetallic core-shell nanoparticle system (FePt@Fe3O4). The signals are decomposed using independent component analysis and the extracted components are used to separately quantify the composition of the spatially overlapping core and shell phases in the nanoheterostructure. The utilization of the complementary strengths of energy dispersive X-ray and electron energy-loss spectroscopy microanalysis has enabled the quantification of both light and heavy elements in a single spectrum image acquisition.