Geologic deposits containing fossils with remains of non-biomineralized tissues (i.e. Konservat-Lagerstätten) provide key insights into ancient organisms and ecosystems. Such deposits are not evenly distributed through geologic time or space, suggesting that global phenomena play a key role in exceptional fossil preservation. Nonetheless, establishing the influence of global phenomena requires documenting temporal and spatial trends in occurrences of exceptionally preserved fossil assemblages. To this end, we compiled and analyzed a dataset of 694 globally distributed exceptional fossil assemblages spanning the history of complex eukaryotic life (~610 to 3 Ma). Our analyses demonstrate that assemblages with similar ages and depositional settings commonly occur in clusters, each signifying an ancient geographic region (up to hundreds of kilometers in scale), which repeatedly developed conditions conducive to soft tissue preservation. Using a novel hierarchical clustering approach, we show that these clusters decrease in number and shift from open marine to transitional and nonmarine settings across the Cambrian-Ordovician interval. Conditions conducive to exceptional preservation declined worldwide during the early Paleozoic in response to transformations of near-surface environments that promoted degradation of tissues and curbed authigenic mineralization potential. We propose a holistic explanation relating these environmental transitions to ocean oxygenation and bioturbation, which affected virtually all taphonomic pathways, in addition to changes in seawater chemistry that disproportionately affected processes of soft tissue conservation. After these transitions, exceptional preservation rarely occurred in open marine settings, excepting times of widespread oceanic anoxia, when low oxygen levels set the stage. With these patterns, nonmarine cluster count is correlated with non-marine rock quantity, and generally decreases with age. This result suggests that geologic processes, which progressively destroy terrestrial rocks over time, limit sampling of non-marine deposits on a global scale. Future efforts should aim to assess the impacts of such phenomena on evolutionary and ecological patterns in the fossil record.