© 2015 Elsevier Ltd. Mineral-organo associations (MOAs) are a mixture of identifiable biopolymers associated with highly reactive minerals and microorganisms. However, the in situ characterization and correlation between soil organic matter (SOM) and highly reactive Al and Fe minerals are still unclear for the lack of technologies, particularly in the long-term agricultural soil colloids at submicron scale. We combined several novel techniques, including nano-scale secondary ion mass spectrometry (NanoSIMS), X-ray absorption near edge structure (XANES) and confocal laser scanning microscopy (CLSM) to characterise the capacity of highly reactive Al and Fe minerals to preserve SOM in Ferralic Cambisol in south China. Our results demonstrated that: (1) highly reactive minerals were strongly related to SOM preservation, while SOM had a more significant line correlation with the highly reactive Al minerals than the highly reactive Fe minerals, according to the regions of interest correlation analyses using NanoSIMS; (2) allophane and ferrihydrite were the potential mineral species to determine the SOM preservation capability, which was evaluated by the X-ray photoelectron spectroscopy (XPS) and Fe K-edge XANES spectroscopy techniques; and (3) soil organic biopolymers with dominant compounds, such as proteins, polysaccharides and lipids, were distributed at the rough and clustered surface of MOAs with high chemical and spatial heterogeneity according to the CLSM observation. Our results also promoted the understanding of the roles played by the highly reactive Al and Fe minerals in the spatial distribution of soil organic biopolymers and SOM sequestration.