Abstract. Mineral binding is a major mechanism for soil carbon (C) stabilization. However, the submicron information about the in situ mechanisms of different fertilization practices affecting organo-mineral complexes and associated C preservation remains unclear. Here, we applied nano-scale 20 secondary ion mass spectrometry (NanoSIMS), X-ray photoelectron spectroscopy (XPS), and X-ray absorption fine structure spectroscopy (XAFS) to examine differentiating effects of inorganic versus organic fertilization on interactions between highly reactive minerals and soil C preservation. To examine such interactions, soils and their extracted colloids were collected during a 24-year long-term fertilization period (1990-2014) (no-fertilization, Control; chemical nitrogen (N), phosphorus (P) and 25 potassium (K) fertilization, NPK; and NPK plus swine manure fertilization, NPKM). The results for different fertilization conditions showed a ranked soil organic matter (SOM) concentration with NPKM > NPK > Control. Meanwhile, oxalate extracted Al (Alo), Fe (Feo), short range ordered (SRO) Al (Alxps), Fe (Fexps), and dissolved organic carbon (DOC) ranked with NPKM > Control > NPK, but ratios of DOC/Alxps and DOC/Fexps ranked with NPKM > NPK > Control. Compared with the NPK 30 treatment, NPKM treatment enhanced the C binding loadings of Al and Fe minerals in soil colloids at the submicron scale. Furthermore, a greater concentration of highly reactive Al and Fe minerals was present under NPKM than under NPK. Together, these submicron scale findings suggest that both reactive mineral species and their associations with C are differentially affected by inorganic and organic fertilization.