In this paper, a chemically sensitive local characterization technique is used to characterize fullerene peapods containing two metal atoms within each fullerene. By combining bright-field imaging, high-angle annular dark-field imaging, and electron energy loss spectroscopy in a scanning transmission electron microscope, unambiguous identification of the metal atoms present is possible. Key to making this possible is aberration correction, which allows atomic resolution at lower beam energies. The peapods can be imaged for several consecutive scans at 80 keV beam energy, and the combination of techniques allows the position as well as the species of the encapsulated atoms to be identified. Movements of the encapsulated atoms are monitored.