During the Integrated Ocean Drilling Program (IODP) Expedition 347 in 2013, sedimentary records were recovered in the Baltic Sea that cover the Eemian interglacial and Weichselian glacial periods. This non-steady state depositional system was characterized by shifts from limnic to brackish/marine phases over the glacial-interglacial cycle which has subjected the sample location in the Anholt Basin to profound changes in depositional and diagenetic conditions. Here, comprehensive pore-water and solid-phase data of sediments are presented and used to (1) geochemically characterize different depositional environments, (2) identify biogeochemical key processes and (3) reveal the influence of the abundance and reactivity of metal oxide phases on the cycling of iron, manganese and sulfur and the formation of authigenic iron sulfides across depositional boundaries. Due to the steep declining gradient of chloride, at least two limnic phases are recorded in the Anholt Basin sediments which are associated with mostly sandy deposits. Whereas the Ti/Al ratio of the bulk solid phase over the whole sediment core is almost constant, suggesting mostly uniform composition and steady erosion on land, the availability of iron and manganese oxides – predominantly magnetite – is relatively lower in the sandy freshwater deposits. For the mineralization of organic carbon, sulfate reduction is the most dominant process and occurs in several zones whereas the rates of dissimilatory iron and manganese reduction are less significant. The deep, narrow methanic zone is limited by the stoichiometric consumption of methane during AOM-driven sulfate and most probably metal oxide reduction at 93 mcd. Furthermore, the accumulation of significant ferrous iron in the pore water is attributed to the dissolution of abundant clay minerals. Sulfide is absent throughout the entire sediment core as it is scavenged immediately after release to form iron sulfides with abundant ferrous iron. Sedimentary boundaries from limnic to marine conditions are subjected to the focused enrichment of authigenic iron sulfides whereas the high degree of diagenetic overprint is indicated by significant contents of pyrite at the MIS 5e – MIS 5b/d and MIS 2 – MIS 1 boundaries. Based on the enrichment of iron sulfides at the MIS 5b/d – MIS 5a boundary, a relict SMT has been preserved over prolonged time scales whereas the upward directed migration of methane shifted the recent SMT to the MIS 5a – MIS 4 boundary. Due to the lack of free sulfide in iron-dominated sediments, the formation of iron phosphate minerals might be an additional sink for ferrous iron below 23 mcd.