The broad-scale environment plays a substantial role in shaping modern marine ecosystems, but the degree to which palaeocommunities were influenced by their environment is unclear. To investigate how broad-scale environment influenced the community ecology of early animal ecosystems, we employed spatial point process analyses (SPPA) to examine the community structure of seven late Ediacaran (558–550 Ma) bedding-plane assemblages drawn from a range of environmental settings and global localities. The studied palaeocommunities exhibit marked differences in the response of their component taxa to sub-metre-scale habitat heterogeneities on the seafloor. Shallow-marine (nearshore) palaeocommunities were heavily influenced by local habitat heterogeneities, in contrast to their deeper-water counterparts. The local patchiness within shallow-water communities may have been further accentuated by the presence of grazers and detritivores, whose behaviours potentially initiated a propagation of increasing habitat heterogeneity of benthic communities from shallow to deep-marine depositional environments. Higher species richness in shallow-water Ediacaran assemblages compared to deep-water counterparts across the studied time-interval could have been driven by this environmental patchiness, because habitat heterogeneities increase species richness in modern marine environments. Our results provide quantitative support for the ‘Savannah’ hypothesis for early animal diversification—whereby Ediacaran diversification was driven by patchiness in the local benthic environment.