An unprecedented period of phosphogenesis, along with massive deposition of black shales, major perturbations in the global carbon cycle and the rise of atmospheric oxygen, occurred in the terminal Proterozoic in the aftermath of the Marinoan glaciation. Although causal links between these processes have been postulated, evidence remains challenging. Correlated in situ micro-analyses of granular phosphorites from the Ediacaran Doushantuo Formation in Yichang, South China, suggested that cyanobacteria and associated extracellular polymeric substances (EPS) might have promoted aggregated granule growth and subsequent phosphatization (She et al., 2013). Here, we present new paleontological data for the Doushantuo phosphorites from Yichang, which, combined with Raman microspectroscopy and carbon isotope data, further document links between the biology of cyanobacteria and phosphogenesis. Mapping of microfossils in thin section shows that most phosphatic granules contain microfossils that are dominated by colonies of Myxococcoides, along with several filamentous genera generally considered to represent cyanobacterial sheaths. In addition, the phosphorites and associated rocks have δ13Corg values in the range of −26.0 to −29.7‰ VPDB, consistent with photoautotrophic carbon fixation with the Rubisco enzyme. Close association of phosphorites with the Marinoan tillites in stratigraphic level supports a genetic link between deglaciation and phosphogenesis, at least for the Doushantuo occurrence. Our new data suggest that major cyanobacterial blooms probably took place in the terminal Proterozoic, which might have resulted in rapid scavenging of bioavailable phosphorus and massive accumulations of organic matter (OM). Within a redox-stratified intra-shelf basin, the OM-bound phosphorus could have liberated by microbial sulfate reduction and other anaerobic metabolisms and subsequently concentrated by Fe-redox pumping below the chemocline. Upwelling of the bottom waters or upward fluctuation of the chemocline might have brought P-enriched waters to the photic zone, where it was again scavenged by cyanobacteria through their EPS to be subsequently precipitated as francolite. The feedbacks between enhanced continental weathering, cyanobacterial blooms, carbon burial, and accelerated phosphorus cycle thus controlled the marine biogeochemical changes, which led to further oxygenation of the atmosphere and oceans, ultimately paving the way for the rise of metazoans.