Iron (Fe) oxyhydroxides can be reductively dissolved or transformed under Fe reducing conditions, affecting mineral crystallinity and the sorption capacity for other elements. However, the pathways and rates at which these processes occur under natural soil conditions are still poorly understood. Here, we studied Fe oxyhydroxide transformations during reduction-oxidation cycles by incubating mesh bags containing ferrihydrite or lepidocrocite in paddy soil mesocosms for up to 12 weeks. To investigate the influence of close contact with the soil matrix, mesh bags were either filled with pure Fe minerals or with soil mixed with 57Fe-labeled Fe minerals. Three cycles of flooding (3 weeks) and drainage (1 week) were applied to induce soil redox cycles. The Fe mineral composition was analyzed with Fe K-edge X-ray absorption fine structure spectroscopy, X-ray diffraction analysis and/or 57Fe Mössbauer spectroscopy. Ferrihydrite and lepidocrocite in mesh bags without soil transformed to magnetite and/or goethite, likely catalyzed by Fe(II) released to the pore water by microbial Fe reduction in the surrounding soil. In contrast, 57Fe-ferrihydrite in mineral-soil mixes transformed to a highly disordered mixed-valence Fe(II)-Fe(III) phase, suggesting hindered transformation to crystalline Fe minerals. The 57Fe-lepidocrocite transformed to goethite and small amounts of the highly disordered Fe phase. The extent of reductive dissolution of minerals in 57Fe-mineral-soil mixes during anoxic periods increased with every redox cycle, while ferrihydrite and lepidocrocite precipitated during oxic periods. The results demonstrate that the soil matrix strongly impacts Fe oxyhydroxide transformations when minerals are in close spatial association or direct contact with other soil components. This can lead to highly disordered and reactive Fe phases from ferrihydrite rather than crystalline mineral products and promoted goethite formation from lepidocrocite.