According to prior laboratory research evidence, the formation of a conductive secondary mineral to accelerate electron transfer is an important factor in methanogenesis. However, the promotion of methanogenesis by a secondary mineral is rarely found in the in situ terrestrial ecosystem. In this study, soil samples with a depth profile were collected from a wetland in the Yellow River Delta (YRD), in which a special red clay horizon (RCH) widely exists. By analysing the soil physicochemical properties and microbial diversity, we demonstrate that the RCH is distinguished from its upper and lower layers by increased iron oxides and a higher abundance and diversity of electrogenic bacteria and methanogens. Further experimental results demonstrate that the RCH soil presented the lowest level of iron reduction ability and the highest methane production rate. Meanwhile, the precipitation of magnetite appeared in the treatment with the RCH soil as an inoculum. In the third generation of the RCH enrichment, the iron reduction ability was further suppressed, and the methane production rate was increased. Accordingly, changes to the microbial community structure were observed, manifested as a marked increase in the abundance of bacteria with the capacity to release electrons, such as Thermincola, Rombotusia, and Shewanella, as well as Methanosarcina, an archaea known as an electron-accepting methanogen. This study suggests that the RCH benefits the syntrophy between electron-donating and electron-accepting partners with the assistance of biologically diagenetic magnetite. To our knowledge, this is the first exploration for the promotion of methanogenesis by a biogenic mineral in the in situ critical zone.