The composition and distribution of elements within cells of two species of Fe and S oxidising microbes utilising S, Fe2+ or chalcopyrite (CuFeS2) as an energy source were compared to determine possible sites of oxidation and function of intracellular granules. The bacterium Acidithiobacillus ferrooxidans and the archaeon Metallosphaera hakonensis were examined using energy filtered transmission electron microscopy (EFTEM), TEM energy dispersive X-ray spectroscopy (EDS), Scanning TEM (STEM) and electron energy-loss spectroscopy (EELS). Both species have intracellular granules and we show that these store Fe, S and P. The microbes slowly lost Fe from granules when switched to an Fe-free medium. EELS showed that the Fe in the granules of both species was consistent with Fe3+. Both microbes sometimes contain Cu and Si on their walls and intracellularly. Si concentrations have been shown to affect bioleach performance, so element deposition on the microbial catalyst may be a reason for this. Bands of Fe and S were present close to, or in, the cell membrane of M. hakonensis, as might be expected for the site of oxidation, and S also occurred throughout the cytoplasm. These are the first element maps of M. hakonensis, and these early results demonstrate that advanced characterisation and microanalysis techniques can provide insights into microbial processes involved in bioleaching.