Abstract The stratigraphic fill of incised valleys has traditionally been interpreted to be primarily modulated by allogenic controls. The use of this concept has been so dominant that the possibility of autogenic mechanisms controlling fluvial organization of incised valley fills (IVFs) is largely overlooked, particularly in rock-record interpretations. This has been mainly due to the fact that deconvolving autogenic from allogenic signals remains challenging, especially for IVF deposits. Using integrated light detection and ranging (LiDAR), outcrop, and core data, we investigated the fluvial architecture of two IVFs in the lower Blackhawk Formation (Upper Cretaceous) of the Western Interior Seaway, Utah. Contrary to conventional interpretation, our analyses demonstrate that an autogenic signal linked to differential compaction of coal-precursor peats underlying IVFs likely exerted substantial control in both the vertical and lateral organization of sand-body architecture in these two IVFs, which are up to ~15 to 20 m thick individually. Trends in vertical-amalgamation thickness, number of channel-story sand bodies stacked vertically, and width constraints of multilateral sand bodies (lateral amalgamation) of these two IVFs are correlated with thickness variation of underlying coal seams. Decompaction analysis of coal seams indicates that the magnitude of accommodation-creation by coal-precursor peat compaction was potentially much higher to overcome allogenic modulation. This is invoked as the principal reason for broad correlation between fluvial architecture of the IVFs and coal thickness in our data set. These findings contribute to isolating autogenic from allogenic signals in complex systems such as IVFs. They further provide insights on signal-shredding mechanisms in the depositional architecture of the Cretaceous Western Interior Seaway, and they supply evidence that paleovalley fluvial architecture should not be automatically attributed to allogenic processes.