Microbialite microstructures form at the scale of microbial processes and can preserve evidence of growth, degradation, and lithification in microbial communities. Understanding how these processes are preserved in microstructures will provide insights into microbial ecosystems and how microbial communities have evolved through time. Microbialites in the Neoproterozoic Beck Spring Dolomite, southern California, U.S.A., contain microstructures that record variations in the morphology of microbial communities as well as the timing of degradation versus lithification in the communities. These processes are represented by five end-member microbial microstructures: 1) distinct laminated microstructure; 2) diffuse laminated microstructure; 3) distinct clotted microstructure; 4) diffuse and regular clotted microstructure; and 5) diffuse and irregular clotted microstructure. These microstructures are distinguished by fabrics defined by organic inclusions. In distinct microstructures, organic inclusions sharply define microbial features, such as laminae that are laterally continuous for millimeters or 50–200 micron diameter microclots. The contacts between distinct microstructures are always sharp. In diffuse microstructures, zones of organic inclusions lack distinct boundaries; neighboring laminae and clots grade into each other within tens of microns, and boundaries between microbial structures and encasing cements are indistinct. Diffuse microstructures grade into each other and into distinct microstructures in a systematic way that suggests that differences are due to variations in the timing of mineralization relative to growth and degradation of microbial communities. Sharply defined textures in distinct microstructures suggest that lithification started during growth of the microbial community, and the close spatial association but lack of intergrading between distinct laminated and distinct clotted microstructures suggests that they formed from two distinct microbial communities that lived in the same environment. By contrast, diffuse microstructures formed where lithification occurred after the onset of decay and degradation of the primary growth structure. The continuum from distinct microbial textures through more diffuse and irregular textures documents variations in the timing of lithification relative to growth and decay of the microbial community. Thus, where petrographic preservation is extremely good, such as in the Beck Spring Dolomite, sub-millimeter-scale microbial microstructures record a gradation between growth and degraded microbial structures depending on the relative timing of lithification and heterotrophic decay.