Visualizing atoms and discriminating between those of different elements is a goal in many analytical techniques. The use of electron energy-loss spectroscopy (EELS) in such single-atom analyses is hampered by an inherent difficulty related to the damage caused to specimens by incident electrons. Here, we demonstrate the successful EELS single-atom spectroscopy of various metallofullerene-doped single-wall nanotubes (known as peapods) without massive structural destruction. This is achieved by using an incident electron probe with a low accelerating voltage (60 kV). Single calcium atoms inside the peapods were unambiguously identified for the first time using EELS. Elemental analyses of lanthanum, cerium and erbium atoms were also demonstrated, which shows that single atoms with adjacent atomic numbers can be successfully discriminated with this technique.