We have identified millennial-scale variations in magnetic mineral diagenesis from Pacific Ocean sediments offshore of Japan that we correlate with changes in organic carbon burial that were likely driven by Asian monsoon fluctuations. The correlation was determined by identifying offsets between the positions of fossil diagenetic fronts and climatically induced variations in organic carbon burial inferred from magnetic and geochemical analyses. Episodes of intense monsoon activity and attendant sediment magnetic mineral diagenesis also appear to correlate with Heinrich events, which supports the existence of climatic telecommunications between Asia and the North Atlantic region. Several lines of evidence support our conclusions: (1) fluctuations in down-core magnetic properties and diagenetic pyrite precipitation are approximately coeval; (2) localized stratigraphic intervals with relatively stronger magnetic mineral dissolution are linked to enhanced sedimentary organic carbon contents that gave rise to nonsteady state diagenesis; (3) down-core variations in elemental S content provide a proxy for nonsteady state diagenesis that correlate with key records of Asian monsoon variations; and (4) relict titanomagnetite that is preserved as inclusions within silicate particles, rather than secondary authigenic phases (e.g., greigite), dominates the strongly diagenetically altered sediment intervals and are protected against sulfidic dissolution. We suggest that such millennial-scale environmental modulation of nonsteady state diagenesis (that creates a temporal diagenetic filter and relict magnetic mineral signatures) is likely to be common in organic-rich hemipelagic sedimentary settings with rapidly varying depositional conditions. Our work also demonstrates the usefulness of magnetic mineral inclusions for recording important environmental magnetic signals.