The morphological properties, the mineralogy, and the chemical composition of Mn‐Fe nodules, collected from an Alfisol in Southern China (Wuhan), were studied by optical microscopy (OM), transmission electron microscopy (TEM), and scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), total and sequential dissolution chemical analyses and differential x‐ray diffraction (DXRD). This information is needed to gain a further understanding of nodule formation in soil environments and the influence of Mn and Fe oxides on the phyto‐availability of both nutrients and toxic trace metals. Element quantification and mapping showed that Si, Al, Fe, Mn, Ca, K, and Ti were the main elements present in the nodules. Nodules were found to be highly variable in composition and in degree of banding of Fe and Mn. In spherical nodules, Fe and Mn were distributed mainly in concentric bands. With few exceptions, heavy metals were concentrated in the finest fraction (<2 μm). Copper and Ni were associated mainly with Mn, whereas Cr and V were associated with Fe. The majority (90%) of total Fe in the <2‐μm fraction was extracted by ammonium oxalate and dithionite reagents. Most (61%) of total Mn was dissolved by hydroxylamine hydrochloride. It was ascertained by DXRD analysis that ferryhydrite and goethite were the poorly crystalline and crystalline Fe phases, and that lithiophorite and vernadite were the Mn oxides. Micromorphological, chemical, and mineralogical results suggest that the growth of nodules was initiated by flocculation of phyllosilicates in oxidative environments. The MnO2 minerals may have inhibited recrystallization of the ferryhydrite.