Thrombolite reefs with archaeocyaths are common in the subtidal limestones of the lower Cambrian in the western Anti-Atlas of Morocco. The Igoudine Formation of the Tata Group recorded the first replacement of the microbial consortium (stromatolite-dominated) by thrombolite reefs with archaeocyaths and shelly metazoans. In order to better understand the role of the microbial community in the formation of thrombolite reefs with archaeocyaths across this critical transition, the macro-, micro- and ultra-fabric of thrombolites have been studied in detail. Three major components are identified within the first thrombolytic reef: archaeocyaths, calcimicrobes and micritic matrix. The studied thrombolites are typically dominated by the calcimicrobe Renalcis with subordinate Epiphyton and Girvanella. Scanning electron microscopy of the dark micrite of the Renalcis chambers showed amorphous translucent sheet-like structures interpreted as extracellular polymeric substances, closely associated with organominerals including nanoglobules and polyhedrons. Exceptionally well-preserved Renalcis chambers contain bacterial fossils similar to those described in modern microbialites, including microspherical coccoid fossils and filamentous bacteria that are either spaced or in close associations forming colonies. These organomineralization-related features suggest a bacterial origin for the Renalcis calcimicrobe. The matrices between the Renalcis chambers consist predominantly of clotted peloidal micrite. Mineralization of Renalcis microframes may involve two major biomineralization processes: (1) replacement of organic matter by organominerals resulting from anaerobic degradation of extracellular polymeric substances and bacterial sheaths and (2) encrustation of bacterial sheaths and extracellular polymeric substances due to increasing alkalinity of the microenvironment. These mechanisms played a crucial role in the early diagenetic cementation and preservation of the studied reefs.