The chert members of the Paleoproterozoic Gunflint Formation, Ontario, Canada, are commonly regarded as examples of primary silica chemical sediments. This interpretation is founded upon the ubiquitous nature of silica, high fidelity of preservation of microfossils found within, and lack of observed primary carbonate. Previous arguments for silica replacement of carbonate are based on indirect evidence and are largely dismissed. Thus, Gunflint microfossils are regarded as having lived in a silica-rich environment, which makes them unusual compared to most other pre-Phanerozoic microfossils that are known from silicified carbonates. We present evidence that carbonate was a primary mineral species of the Lower Algal Chert Member (where most of the microbiota are found). Most compelling are iron-stained, low-Mg calcite ooids containing (1) well-preserved growth laminae, (2) textures indicating a disrupted tangential fabric of growth laminae, and (3) quartz crosscutting the growth laminae. These indicate the initial mineral was a carbonate, possibly aragonite. Less-compelling evidence is found in stromatolite columns. Specularite crystals in low-Mg calcite display crosscutting relationships with calcite and quartz indicating that calcite was primary, specularite secondary, and quartz tertiary. The crosscutting relations show that silicification took place in at least two stages. One of the silicification events took place very early in diagenesis. Thus the Gunflint microbiota may not have existed in a radically different environment (silica precipitating) than those of most other known Proterozoic microbiota. High fidelity of preservation of microfossils does not always indicate that the mineral entombing them was the primary mineral precipitated from aqueous solution.