The metallome has been defined as the distribution of metals and metalloids among the different species and cell compartments. The detection of trace elements at the subcellular level is a challenging task that requires sophisticated analytical developments. In this study, we report how chemical element imaging was performed in subcellular compartments of dopaminergic cells at high spatial resolution using the X-ray fluorescence nanoprobe recently developed at the European Synchrotron Radiation Facility. High spatial resolution is obtained using the concept of a secondary source focused to a 90 nm probe by multilayer mirrors bent in Kirkpatrick–Baez geometry. This original setup was applied for trace metal mapping of single dopaminergic cells, chosen as an in vitro model of degenerative cells involved in Parkinson's disease. This cellular model is able to differentiate upon exposure to nerve growth factor and to extend neurite-like processes. Two important results were obtained. First, iron is distributed in a granular form into dopamine vesicles, found mainly in primary neurite outgrowths and distal ends. Second, thin neurite-like processes produced by differentiated cells accumulate copper, zinc, and to a minor extent lead. Overall, the high resolution imaging of single neuronal cells offers unique information to understand the role of trace metals in neurochemistry.