Abstract Microbialites are the most abundant life evidence in Precambrian sedimentary rocks. They are produced by microbial interaction activity and sedimentary processes reflecting paleoenvironmental conditions. The Ediacaran-Cambrian carbonate and siliciclastic successions in the Southern Amazon Craton in Central Brazil, provide a key opportunity to understand how the metazoan life coexisted with the microbial communities. The spatial and temporal distribution of microbialites as well as morphological and paleoenvironmental changes have been assessed, reinterpreting previous works and including new data from the Araras-Alto Paraguai and Corumbá basins. The deposition was controlled by subsidence and sea-level changes that affected these basins, considered extensions of epicontinental seas during the Gondwana assembly. The stromatolites are restricted to coastal deposits and experienced thriving flourishment intervals after the Marinoan Glaciation (635 Ma). Post-glacial transgression was marked by microbial colonization in shallow platforms represented by stratiform and giant domical stromatolites in the Araras-Alto Paraguai Basin. The continuity of the transgression generated a moderately deep aragonite sea at about 622 Ma. A progressive sea-level fall caused the implantation of coastal environments under greenhouse conditions with tidal flat and sabkha settings colonized by centimetric-scale stromatolites. The sea retreat was accompanied by progressive uplift, causing a moderate inversion of the basin and erosion of the succession until ~560 Ma with the deposition of the last preserved tidal flat deposits with the occurrence of thrombolites. The subsiding Corumbá Basin was the site of microbially-induced deposition of carbonates in a shallow platform connected to an offshore setting with the proliferation of metazoan straddling the Ediacaran-Cambrian boundary. Microbial communities were restricted to lagoon deposits during the Lower Cambrian transgression in the Araras-Alto Paraguai Basin and the last phase refers to the sea retreat towards southeast, developing a fluvial system connected with the arid and evaporitic tidal flats colonized by microbialites that lasted until the upper Cambrian. Except for the post-glacial stromatolites, the columnar and domal microbialite indicate that the coastal settings dominated the Ediacaran-Cambrian transition. The preservation of microbialites in the post-glacial intervals can be associated with the Mg-Ca-CO3 oversaturation in dolomitic platforms. The rapid calcification and ability to resist the dissolution and replacement have increased the stromatolites’ preservation potential reported here, where its well-preserved occurrence in tidal flats and sabkha occurs due to intense early diagenetic silicification. The change from carbonate accumulation to siliciclastic-rich environments contributed to the demise of microbially-induced strata. In general, the scarce coexistence between coastal stromatolite and metazoan-bearing marine deposits makes it challenging to establish a competitive relationship between these organisms, as previously postulated.