Evidencing ancient interspecific associations in the fossil record may be challenging, particularly when bacterial organisms have most likely been degraded during diagenesis. Yet, documenting ancient interspecific associations may provide valuable insights into paleoenvironmental conditions and paleocommunities. Here, we report the multiscale characterization of contemporary and fossilized calcifying bacterial colonies found on contemporary shrimps from Mexico (La Paz Bay) and on 160-Ma old fossilized decapods (shrimps) from the Lagerstätte of La Voulte-sur-Rhône (France), respectively. We document the fine scale morphology, the inorganic composition and the organic signatures of both the contemporary and fossilized structures formed by these bacterial colonies using a combination of electron microscopies and synchrotron-based scanning transmission X-ray microscopy. In addition to discussing the mechanisms of carbonate precipitation by such bacterial colonies, the present study illustrates the degradation of bacterial remains occurring during diagenesis.