Mineral infill of bones can vary significantly among specimens from the same formation, suggesting that early-diagenetic, authigenic processes may be as or more important to preservation than pervasive, late-diagenetic lithification. Archeological and forensic studies suggest that diagenesis occurring immediately post-mortem, before permanent burial, is critical, and can ultimately dictate bone preservation. To test this concept in a fully lithified deep-time record, we tested for diagenetic variation in whale bones collected from different positions within a 3^rd-order depositional sequence from the Eocene of Egypt (Valley of the Whales): if early diagenesis dominates, then infills and bone tissue preservation would vary as a function of depositional rates and environments. Bones associated with the maximum flooding surface (MFS) should experience significantly longer exposure at the sediment-water interface and within the taphonomically active mixed layer, resulting in higher geochemical complexity and increased taphonomic damage than bones from within a transgressive or highstand systems tract, where burial rates are higher and homogenous preservation is expected. Bones associated with a sequence boundary (SB) should present features unique to erosional reworking and mineral alteration linked to subaerial exposure. Thin-sections of vertebral bones were examined petrographically and with mXRF to map chemical heterogeneity within each bone. We find that the dominant authigenic mineral composition within each bone does differ significantly across the depositional sequence. Samples from the MFS yield a complex celestine-dominated infill with poor morphological preservation quality, those from the SB are dominated by dolomite with a significant amount of small-scale fracturing within bone tissue, and those from within systems tracts are dominated by iron-rich calcite and gypsum infill. The heterogeneity found here, and its close relationship to sequence stratigraphic context, indicates a geochemically complex system where diagenetic infill is determined by pre-burial conditions, and that this signature from authigenic processes survives subsequent post-depositional lithification processes.