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).