The bioavailability of trace elements in the course of evolution had an essential influence on the emergence of life itself. This is reflected in the co-evolution between eukaryotes and prokaryotes. In this study, the influence and cellular distribution of bioelements during phagocytosis at the host-pathogen interface were investigated using high-resolution nanoscale secondary ion mass spectrometry (NanoSIMS) and quantitative inductively coupled plasma mass spectrometry. In the eukaryotic murine macrophages (RAW 264.7 cell line), the cellular Fe/Zn ratio was found to be balanced, whereas the dominance of iron in the prokaryotic cells of the pathogen Salmonella enterica Serovar Enteritidis was ∼90% compared to zinc. This confirms the evolutionary increased zinc requirement of the eukaryotic animal cell. Using NanoSIMS, the Cs+ primary ion source allowed high spatial resolution mapping of cell morphology down to the subcellular level. At a comparable resolution, several low-abundant trace elements could be mapped during phagocytosis with a RF plasma O- primary ion source. An enrichment of copper and nickel could be detected in the prokaryotic cells. Surprisingly, an accumulation of cobalt in the area of the nuclear envelope was observed, indicating an interesting but still unknown distribution of this trace element in murine macrophages. © The Author(s) 2022. Published by Oxford University Press.