A soil chronosequence from the River Guadalquivir (Spain) was studied at a nanometre scale (10−9 m), this being a poorly investigated aspect of soil genesis. The fine mineral fractions (< 50 μm) were studied by X-ray diffraction (XRD) and analytical electron microscopy (TEM-AEM). At a nano-scale, the dominant materials in the chronosequence were dioctahedral 2:1 phyllosilicates, such as potassium mica (mainly muscovites and illites), mixed-layer smectite/illite and smectite (beidellite). Sodium mica brammallite was described for the first time in soils. These dioctahedral phases are related genetically to illite by inheritance of muscovite and posterior transformation of illite into beidellite. These processes involve (i) loss of regularity in the layer stacking sequence in high-resolution TEM images, even to the point of losing the contrast between layers; (ii) loss of three-dimensional order in selected area (electron) diffraction (SAED) patterns, with increased diffusivity and weak spots on hkllevels; (iii) smaller layer packets producing superimposed SAED patterns (high-angle boundaries in 00l); (iv) changing from two-layer ordered polytypes (2M1) to one-layer random polytypes (1Md); and (v) chemically, loss of charge and ions in the interlayer. The final result is beidellites with almost tactoid morphologies. As these processes are related to the soil-forming factor of time it was possible to establish logarithmic chrono-functions tending to steady state for nano-scale properties such as the percentage of 2M1 polytypes, the layer charge, interlayer charge and the interlayer ion content in 2:1 phyllosilicates (more smectite-like micas). This shows that time affects soil-forming processes at the nano-scale to the same extent as described for other scales such as ultra-microfabric (10−6 m), horizon (10−1 m) or pedon (100 m).