Changes in stable chromium isotopes (denoted as δ53Cr) in ancient carbonate sediments are increasingly used to reconstruct the oxygenation history in Earth’s atmosphere and oceans through time. As a significant proportion of marine carbonate older than the Cambrian is microbially-mediated, the utility of δ53Cr values in ancient carbonates hinges on whether these sediments accurately capture the isotope composition of their environment. We report Cr concentrations (Cr) and δ53Cr values of modern marginal marine and non-marine microbial carbonates. These data are supported by stable C and O isotope compositions, as well as rare earth elements and yttrium (REY) concentrations. In addition, we present data on ancient analogs from Precambrian strata. Microbial carbonates from Marion Lake (Australia, δ53Cr ≈ 0.99‰) and Mono Lake (USA, ≈0.78‰) display significantly higher δ53Cr values compared with ancient microbialites from the Andrée Land Group in Greenland (720 Ma, ≈0.36‰) and the Bitter Springs Formation in Australia (800 Ma, ≈−0.12‰). The δ53Cr values are homogenous within microbialite specimens and within individual study sites. This indicates that biological parameters, such as vital effects, causing highly variable δ53Cr values in skeletal carbonates, do not induce variability in δ53Cr values in microbialites. Together with stable C and O isotope compositions and REY patterns, δ53Cr values in microbialites seem to be driven by environmental parameters such as background lithology and salinity. In support, our Cr and δ53Cr results of ancient microbial carbonates agree well with data of abiotically precipitated carbonates of the Proterozoic. If detrital contamination is carefully assessed, microbialites have the potential to record the δ53Cr values of the waters from which they precipitated. However, it remains unclear if these δ53Cr values record (paleo-) redox conditions or rather result from other physico-chemical parameters.