Innovative microanalytical methods are valuable tools in geomicrobiology. They often require the use of dried samples, demanding a challenging sample preparation. Since geomicrobiological samples typically have a strongly heterogeneous composition, choosing a preparation method is not straightforward. We therefore compared how different drying methods (critical point drying, hexamethyldisilazane drying, air drying, and freeze drying) influence the structure of bacterial cell-mineral aggregates. Each method proved suitable for a specific purpose, but none were able to completely preserve the sample structure. Additional information was obtained on surface alterations by sputter coating and on preservation of extracellular polymeric substances during resin embedding.