Fossil microbes are generally preserved by authigenic minerals, including silica, apatite, iron minerals, clays, and carbonates. An alternative mode of preservation by entombment in calcite, without replacement, has been identified in carbonate cave pool microbialites that were etched and examined in the scanning electron microscope (SEM). Features identified include filaments, threads, and films that show excess carbon in energy dispersive X-ray (EDX) analyses, suggesting preservation of organic matter. Filaments are single smooth or reticulated strands with curving string-like morphology, often hollow, and with a uniform diameter of 0.5 to 1.0 μm. Threads, in contrast, are variable thickness, from several microns down to 0.1 μm, always solid, and commonly branch. Films are thin (< 1 μm) drapes associated with threads. Filaments are interpreted as microbial filaments, while threads and films are interpreted as preserved extracellular polymeric substance (EPS). In addition, microbial filaments and EPS are only revealed via acid etching, suggesting preservation of organic material by entombment, not by replacement with calcite. To determine whether entombed microbes are a common feature of carbonate microbialites that form in different environmental settings, samples of hot spring travertine, caliche soil, and reef microbialite were examined. Whereas the travertine samples were barren, entombed EPS was found in the caliche soil and the reef microbialite; the latter also contained a few entombed filaments. In addition, entombed microbial material has been reported from carbonate cold seep deposits. Such findings indicate that entombment of microbes and EPS in carbonates is not restricted to cave settings, but is more widespread than previously reported. Possible causes for the lack of preservation in travertines include rapid degradation of microbial material either by sunlight due to photolytic degradation, aerobic microbial degradation, detritivore consumption, or elevated temperatures. Rapid carbonate precipitation is ruled out as, somewhat surprisingly, preservation is better in slower growing cave carbonates than in rapidly growing travertines. Potential long-term preservation of organic material entombed in carbonate has implications for the characterization of fossil microbial communities using molecular biomarkers and the search for life on other planets.