Interchanging submergence and drainage in paddy soils induce alternating redox conditions. It is known that this causes changes in organic carbon stocks, in amounts and crystallinity of Fe oxides as well as transformation of clay minerals and subsequent changes in cation exchange capacity (CEC). However, the influence of the initial soil type on the extent of these changes is not yet well understood. Therefore, we studied paddy soils that derived from three different soil types (Vertisols, Andosols, Alisols) on volcanic parent material in Java (Indonesia). To account for the variability in parent materials, we additionally sampled sandstone-derived Alisols in China. Adjacent non-paddy soils were sampled as references. Samples were analyzed for texture, bulk density, clay mineral composition, total element content, pH, CEC, phosphorus retention, organic carbon (OC), and acid oxalate- (Feox) and dithionite–citrate–bicarbonate-extractable Fe (FeDCB).Only the Alisol-derived paddy soil in China showed textural changes, compared to the non-paddy soil. Evidence for paddy management induced ferrolysis was not found. The smaller topsoil clay content in the paddy soil is most probable caused by clay migration. Only minor differences in clay minerals were found; topsoils of Andosol-derived paddy soils, however, tend to be less desilicated, indicating phytolith accumulation. Except for Vertisols, paddy management caused significant depletion in Fe oxides in the topsoils (puddled layer and plow pan) due to redox processes. The extent to which the reduced Fe was leached or re-oxidized as short range-ordered Fe oxides depended on the soil texture. Andosols and sandy Alisols facilitated leaching, clayey Alisols re-oxidation. In either case, the stocks of crystalline Fe oxides diminished, causing increased proportions of short range-ordered Fe oxides. Retention of phosphorus was directly related to changes in the absolute amounts of short range-ordered Fe oxides. An accumulation of Fe oxides in paddy subsoils was not found. Lateral transport with drainage water might be a reason. In highly permeable soils with large vertical water fluxes (e.g., Andosols under paddy management), colloidal transport might also play a role. Despite losses in potential OC storage capacity (i.e., Fe oxides, clay minerals, allophane), paddy soils derived from Andosols and sandy Alisols in China had larger OC concentrations in the puddled topsoil, whereby the other soils showed no increase in OC under paddy management. Therefore, paddy management does not necessarily enhance carbon sequestration. Rather, differences in organic matter input between non-paddy and paddy soils seem to determine whether OC is accumulated under paddy management or not. Effects of paddy management on CEC were little and mainly due to OC accumulation and Fe oxide coating removal from clay minerals.Overall, paddy management-induced changes were partly influenced by the original soil and the parent material. In turn, the main characteristics of the initial soil type were preserved and not overridden by paddy management.