These are data files and images interpreted and presented in the publication of "Imaging biomineralizing bacteria in the native-state with X-ray fluorescence microscopy" by Chevrier et al. Chemical Science 2025; DOI: 10.1039/D4SC08375J. All datasets are representative for the figures and data presented in the publication. For those interested in more information on the datasets, please contact the creator. Files with "Afterbeam..." and "Control" are epifluorescence images for the live-dead assay.Files with "0uMFe...", "10uMFe..." and "50uMFe..." are from bacterial samples grown with different concentrations of iron in the growth medium (see publication). Most of the files are nano-XRF images from Fe Ka emission with associated Figure number in the manuscript. The condition is also given (e.g., dried or liquid). TEM images are also provided for each iron concentration condition. Files labelled with "Insitu..." are all nano-XRF images from the Fe Ka emission. Lastly, ascii files are provided for X-ray absorption spectra presented in the paper.