We evaluated the impact of nano-structural characteristics of allophanic compounds and Fe oxide speciation on the efficiency of organo-mineral interactions in an allophanic Andosol derived from volcanic ash (Eifel mountains, Germany). The samples selected for our work represented a gradient from: (i) a pure synthetic allophane and (ii) model organo-mineral mixtures to (iii) particle size fractions of the natural Andosol. We thus aimed to link the processes operating at the individual molecular scale to the phenomena active at the aggregate scale. For a non-destructive characterization of the samples, we applied 129Xe NMR spectroscopy of adsorbed Xe atoms (to identify the mineral nano-structure and surface acid centres), ESEM (verifying the nano-spherical structure of allophane), 13C CPMAS NMR (for the nature of the soil organic matter (SOM)), 57Fe Mössbauer spectroscopy (Fe oxide speciation), and N2 adsorption (contribution of micro- and mesoporosity). By using the atomic probe Xe, we obtained evidence for a coupled mechanism of adsorption onto allophane requiring both the narrow pores (voids formed by the primary nano-spherules) and the acid centres located at the defect surfaces of the primary spherules. The validity of this coupled mechanism for the sorption of organic matter was confirmed by the concomitant blocking of acid centres (129Xe NMR data) and the decrease of the N2-available pore volumes (Vmicro and Vmeso) in the model samples DOM/- and NOM/allophane (DOM=dissolved OM, NOM=natural OM). In the Andosol, the high resistance of SOM against oxidation (OCresist=15–50%) was combined with preferential accumulation of certain organic compounds, e.g. potentially labile substrates such as carbohydrates, and the low molecular weight species such as amino acids. This feature was attributed to the peculiar microporous tortuous structure of allophane aggregates that likely impose certain criteria for the chemical nature and size of mineral-bound SOM. On the other hand, the revealed dominance of nanoparticulate Fe oxyhydroxides (57% ferrihydrite) and Fe-substituted allophane (supposedly formed due to co-precipitation of the Al, Si and Fe in the course of volcanic soil formation) may substantially contribute to the formation of highly resistant organo-mineral associations through the enhanced extent of reactive surface groups in nanoparticles, increased surface charge density and electron accepting properties of substituting Fe3+ species that supposedly enhance the proportion of oxidised organic components.