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Understanding the roles of habitat filtering, dispersal limitations and biotic interactions in shaping the organization of animal communities is a central research goal in ecology. Attempts to extend these approaches into deep time have the potential to illuminate the role of these processes over key intervals in evolutionary history. The Ediacaran marks one such interval, recording the first macroscopic benthic communities and a stepwise intensification in animal ecosystem engineering. Here, we use taxonomic co-occurrence analysis to evaluate how community structure shifted through the late Ediacaran and the role of different community assembly processes in driving these changes. We find that community structure shifted significantly throughout the Ediacaran, with the most dramatic shift occurring at the White Sea–Nama boundary (approx. 550 Ma) characterized by a split between older, more enigmatic taxonomic groups (the ‘Ediacara-type’ fauna) and more recognizable (‘Cambrian-type’) metazoans. While ecosystem engineering via bioturbation is implicated in this shift, dispersal limitations also played apart in separating biota types. We hypothesize that bioturbation acted as a local habitat filter in the late Ediacaran, selecting against genera adapted to microbial mat ecosystems. Ecosystem engineering regime shifts in the Ediacaran may thus have had a large impact on the development of subsequent metazoan communities.