Thin sectioning of organo-mineral nanocomposites enables the elucidation of organic chemistry in their intact structures. Yet its preparation may cause material damage. Using artificial clay-bacteria composites, we showed that thin sectioning using focused ion beam (FIB) caused no significant alternation to carbon (C) chemistry in the composites analyzed by C K-edge spectra with scanning transmission X-ray microscopy with near-edge X-ray absorption fine structure (STXM-NEXAFS), suggesting positive applicability of this approach. Thin sectioning of organo-mineral nanocomposites enables the elucidation of organic chemistry in their intact structures. Yet its preparation may cause material damage. Using artificial clay-bacteria composites, we showed that thin sectioning using FIB caused no significant alternation to carbon (C) chemistry in the composites analyzed by C K-edge spectra with STXM-NEXAFS, suggesting positive applicability of this approach.