The oxygen content of the ocean’s deep waters is declining, threatening valuable marine ecosystems and the ocean’s crucial role in carbon storage. Widely observed banding in marine sediments is believed to be connected to oxygen-sensitive diagenetic processes in shallow sediments. This study combines a spatial survey of distinctive banding in shallow sediments (< 1 meter below seafloor) with novel 1 million-year long records of banding occurrence at International Ocean Discovery Program (IODP) Sites U1474 and U1313 to assess the link between sedimentary diagenetic bands and bottom water oxygen across the middle to late Pleistocene. The spatial survey of banding in shallow sediments indicates that bands at active redox fronts are most clearly connected to high bottom water oxygen concentrations, while the stratigraphic survey shows numerous instances of the synchronous development of banding in both hemispheres during the Pleistocene’s glacial marine isotope stages (MIS) in tandem with low bottom water oxygen events. A review of available evidence suggests that the diagenetic bands form due to rising bottom water oxygen concentrations, which trap reduced iron sourced from organic matter-enriched deposits from a preceding oxygen minimum. Long-eccentricity paced variability in the abundance of bands in both northern and southern hemispheres suggests orbital control on bottom water oxygen and carbon cycle dynamics.