Biogenic sedimentary structures offer a unique perspective for understanding the role of the biosphere in the interaction with other Earth subsystems and the building up of our planet. The record of their ancient equivalents provides a wealth of information for reconstructing the role of bioturbators as ecosystem engineers using multiple ichnological proxies and methods. In this study, we present an overview of how bioturbation has worked across a broad range of spatial and temporal scales from the perspective of ecosystem engineering. Comprehensive and systematic datasets allow analyses at regional and global spatial extents, and especially over long temporal scales where sampling intensity and rock record biases can be considered. Our results underscore the significance of the Cambrian Explosion in the establishment of modern‐style shallow marine ecosystems and of the Ordovician Radiation for their deep marine counterparts, as well as the continuous ecosystem impact of bioturbation during Palaeozoic terrestrialization. Comparable datasets for the rest of the Phanerozoic have not yet been compiled. However, preliminary information indicates that colonization of ultra‐deep tiers, the rise to prominence of regenerators, increased burrowing efficiency, and increased compartmentalization of the endobenthic ecospace, were products of the Mesozoic Marine Revolution. The trace‐fossil record offers hard data to evaluate bioturbation as a driving force in ecosystem re‐structuring and as a key factor in geobiological cycles. Models assessing these fundamental issues should be rooted empirically at different scales, from both autoecological and synecological to macroecological, making the best possible use of the rich and rapidly developing ichnological toolbox.