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The relationship between the emergence of early animal communities around 630 million years ago (Ma) and the oxygenation of the Earth’s environment is the scene of an ongoing controversy. Against a backdrop of progressive ocean oxygenation since the late Neoproterozoic, redox conditions in the subsequent early Cambrian period (541 to 510 Ma), which witnesses the first appearance of widespread animal-dominated ecosystems in the fossil record, are still debated. This is particularly the case for deeper marine settings, where some studies suggest ocean anoxia, whilst others point out fully oxygenated conditions, and the linkage with preserved fossil archives remains, therefore, unresolved. Here, we present inorganic geochemical proxies for ocean redox conditions, coupled with molecular biomarkers and the record of organic walled-fossils in well-constrained stratigraphic successions from the early Cambrian Baltic Basin. We find that the deepest and shallowest environments were oxygenated, whereas mid-depth shelfs were characterized by spatially oscillating anoxic conditions. Analogous to modern oxygen minimum zones (OMZ), this ocean architecture may reconcile the discrepancy between redox signals from individual study sites. Organic remains of benthic fauna were found in association with mildly reducing – rather than oxic – conditions, and we suggest that OMZ dynamics had strong implications on the preservation of thecarbonaceous fossil record.