Poorly crystalline iron (Fe) oxides are commonly deposited on the surface of rice roots, forming an Fe plaque. This Fe plaque is an important area for Fe redox reactions because the poorly crystalline Fe is available for microbial transformations. However, it remains unclear what the mechanisms are that cause the root Fe plaque to affect CO2 emissions from paddy soils. Thus, this study investigated the effects of Fe plaque on paddy soil CO2 emissions and the associated mechanisms. Paddy soil with rice plant roots containing an Fe plaque-coating had 1.5-fold larger CO2 emissions and higher expression levels of genes involved in soil carbon (C) degradation than Fe plaque-free roots, indicating that Fe plaque stimulated paddy soil derived CO2 emissions. Fe plaque-coated rice roots, immersed in a C-13-labeled glucose solution, emitted more CO2, with a higher abundance of (CO2)-C-13, than the Fe plaque-free roots. These differences were not observed when the surfaces of the rice roots were sterilized. These results indicate that the Fe plaque-stimulated CO2 emissions were due to soil microbial respiration, not autotrophic root respiration. Chelating the dissolved Fe on the root surface eliminated Fe plaque stimulation of CO2 emissions, while Fe(III) supplementation correlated with enhanced CO2 emissions. The stoichiometric mole ratio of the enhanced CO2 emissions to the Fe(II) generated was comparable to the theoretical ratio of Fe(III) when used as an electron acceptor for organic C decomposition. These results showed that the Fe plaque enhancement of CO2 emissions was coupled to Fe(III) reduction. Limiting the stimulating effects of Fe plaque on CO2 emissions may be a potentially useful approach for mitigating organic C loss from paddy soils.