The internal structures of commercial spheronised microcrystalline cellulose (s-MCC) and pre-gelatinised starch (PGS) granules were investigated, using a range of methods. Results from scanning electron microscopy (SEM), transmission electron microscopy (TEM) and atomic force microscopy (AFM) revealed hierarchical structures, with dimensions ranging from nanometres to a few micrometres, for both materials. Residual fragments of plant cell walls, consisting largely of crystalline fibrillar bundles, were indicated within s-MCC granules, while PGS granules appeared to consist of densely packed spherical features. The lack of any obvious regular periodicity associated with the intragranular sub-structures was entirely consistent with the power-law behaviour of the small-angle X-ray scattering (SAXS) patterns from these materials. The presence of intragranular porosity was inferred from TEM, AFM and N2-adsorption measurements, while the ability to deform these structures was clearly indicated by the irregular force–displacement curves recorded by AFM on the granule surfaces. Hence, the intragranular sub-structures observed for s-MCC and PGS appeared to be consistent with the possibility of entire granules undergoing affine deformation during compaction. Since this mechanism was postulated to explain changes in SAXS patterns from these materials following compaction, as reported elsewhere, the work reported here provides a considerably stronger basis for using 2D-SAXS to investigate powder compaction behaviour.