The Mozambique continental margin experienced large variations in sedimentation rates, primarily due to re-routing of sediment deposition from the Zambezi River during the last glacial-Holocene transition. As changes in sediment accumulation and organic matter deposition impose a strong control on the formation of authigenic minerals in the sediment, the distribution of these minerals may reflect the regional paleoenvironmental and paleoclimatic evolution. Combining geochemical analyses of porewaters and sediments with a reactive transport modeling approach, we reconstruct the depositional history and its effect on pyrite formation and other biogeochemical transformations at a site on the Mozambique margin over the past 27 kyr. Fitting the model to match the observed geochemical patterns, most importantly authigenic pyrite, allowed for the reconstruction of past sulfate-methane transition zone depth, which migrated in response to changes in the sediment accumulation and organic matter deposition. Changes in sediment deposition quickly affected organoclastic sulfate reduction and associated pyrite formation, but the effect on anaerobic methane oxidation and subsequent pyrite formation occurred with a lag on the order of thousands of years. Model results reveal a transition from high diagenetic reaction rates representative of near-shore depositional environments during the late glacial maximum, to a setting typical of offshore sediments with low reaction rates at the present day. Notably, the remnants of methane and dissolved iron pools produced in the past still shape the diagenetic processes at and below the sulfate-methane transition zone today. Since deglacial shelf-flooding and corresponding changes in sediment deposition occurred along continental margins worldwide, our analysis highlights the important role of non-steady state diagenesis in continental margin sediments and its relevance for paleoceanographic interpretation of sediment cores experiencing strong variations in sediment input.