Rice planting decreased total iron but increased active iron.• Iron activation varied greatly among different paddy soils but not in woodland soils.• Paddy soil iron was mainly affected by pH, SOC and particle composition.• The decrease of soil Fe was mainly in the form of Fe c and was closely related to SOC. Human activities have intensified the activity and morphological transformation of iron in soils, but there is a lack of quantitative assessment of the loss or of the transformation pattern. By studying Fe-rich rice soils in southern China and comparing them with corresponding woodland soils, it was found that rice planting reduced the total iron (Fe t ) content, mainly of crystalline iron (Fe c ), along soil profiles (0−100 cm) while increasing the content of active iron (Fe o ). The activation degree of Fe o (Fe o %) varied significantly among different parent materials in paddy soils but showed less variation in woodland soils. Regression analysis revealed significant correlations between both the content of Fe c and the content of Fe o in paddy soils with soil organic carbon (SOC) and particle composition (p < 0.05). The Fe o % was primarily influenced by pH, SOC, and particle composition. The iron loss in paddy soil was mainly Fe c and was closely related to SOC, whereas the transformation of active iron (Fe o ) was influenced by a combination of soil factors and environmental conditions. The results demonstrate that human activities accelerate the loss and activation of active iron in the soil, thereby altering the iron cycling process in rice paddy ecosystems.