The stabilization of soil organic carbon (SOC) is of fundamental concern in global carbon biogeochemistry. Organic amendments are commonly used for promoting soil fertility, and their impacts on the residual SOC are of both agricultural and environmental interests. SOC associated with minerals is considered to be one of the most fundamental long-term SOC storage strategies, but little research has integrated the organo-mineral complexes regulated by long-term organic amendments. We synthesize information to link the Fe (oxyhydr)oxides, SOC sequestration, and long-term organic inputs from both field and laboratory studies. The results show that vigorous Fe mobilization can be regulated by long-term application of organic amendments, and these organically amended soils contained significantly higher concentrations of poorly crystalline Fe that was closely related to SOC storage in both upland and paddy soils. Potential mechanisms are proposed as follows. DOM extracts from soils treated with organic amendments exhibit a stronger inhibitory effect on the crystallization of poorly crystalline Fe than DOM from inorganically fertilized soils, which may be the consequence of increased numbers of aromatic functional groups. Organic acids in root exudates increased soil mineral availability and the formation of poorly crystalline minerals. Compared to inorganic fertilizers, organic amendments significantly increase (> 20%, p < 0.05) the concentration of poorly crystalline minerals in the presence of actual roots. Besides, microbially-mediated Fe cycling is strongly linked to the Fe mineralogy in soils, and regulated by long-term organic amendments. Greater consumption of poorly crystalline Fe was observed in inorganically-fertilized soil than that in organically amended soil, due to a higher relative abundance of well-known Fe(III) reducers, i.e., Geobacter. Conversely, Fe(II) oxidizers, Anaerolinea and Pseudomonas, were more abundant, and produced higher levels of poorly crystalline Fe under organic amendments.. In conclusion, continuous organic amendments initialize a positive feedback loop for the maintenance of poorly crystalline Fe in soils, which can contribute to enhanced SOC storage.