Active iron oxides, especially poorly crystalline forms, benefit soil organic carbon (SOC) accumulation via directly bounding and indirectly promoting aggregation. However, it remains unclear on the impacts of active iron oxides on SOC accumulation in paddy and upland soils under long-term fertilization regimes. Here, we attempted to clarify the underlying mechanisms of amorphous (FeO) and organically complexed (FeP) iron oxides mediating SOC accumulation in paddy and upland soils based on two long-term fertilization experiments (both including no fertilization [CK]; chemical nitrogen, phosphorus and potassium [NPK] and NPK plus manure [NPKM] treatments). Results showed that compared to upland soil, Fe-bound organic carbon (Fe-bound OC) content in paddy soil, occupying 21–30% of SOC, was 77% higher on average, due to larger amounts of FeO (+31%) and FeP (+224%). The FeO and FeP were positively related to mean weight diameter (MWD) of soil aggregates across paddy and upland soils. Compared to NPK treatment, NPKM treatment strongly increased FeO (+41%), FeP (+60%) and associated Fe-bound OC (+19%) in paddy soil, and increased FeO (+17%) and FeP (+25%) while decreasing Fe-bound OC (–9%) in upland soil. These combined findings indicated the importance of poorly crystalline iron oxides facilitating Fe-bound OC formation and its contribution to SOC accumulation in paddy soil rather than upland soil. Moreover, long-term manure amendment could enhance SOC accumulation by increasing Fe-bound OC and aggregation stability in paddy soil and enhancing physical protection in upland soil, largely attributed to increased poorly crystalline iron oxides. Overall, these results highlight the potential mechanisms through which active iron oxides regulate SOC accumulation and guide fertilization management in paddy and upland soils.