Biochar is often applied to paddy soils as a soil improver, as it retains nutrients and increases C sequestration; as such, it is a tool in the move towards C-neutral agriculture. Nitrogen (N) fertilizers have been excessively applied to rice paddies, particularly in small farms in China, because N is the major limiting factor for rice production. In paddy soils, dynamic changes in iron (Fe) continuously affect soil emissions of methane (CH4) and carbon dioxide (CO2); however, the links between Fe dynamics and greenhouse gas emissions, dissolved organic carbon (DOC), and rice yields following application of biochar remain unclear. The aims of this study were to examine the effects of two rates of nitrogen (N)-enriched biochar (4 and 8 t ha−1 y−1) on paddy soil C emissions and storage, rice yields, and Fe dynamics in subtropical early and late rice growing seasons. Field application of N-enriched biochar at 4 and 8 t ha−1 increased C emissions in early and late rice, whereas application at 4 t ha−1 significantly increased rice yields. The results of a culture experiment and a field experiment showed that the application of N-enriched biochar increased soil Fe2+ concentration. There were positive correlations between Fe2+ concentrations and soil CO2, CH4, and total C emissions, and with soil DOC concentrations. On the other way around, these correlations were negative for soil Fe3+ concentrations. In the soil culture experiment, under the exclusion of plant growth, N-enriched biochar reduced cumulative soil emissions of CH4 and CO2. We conclude that moderate inputs of N-rich biochar (4 t ha−1) increase rice crop yield and biomass, and soil DOC concentrations, while moderating soil cumulative C emissions, in part, by the impacts of biochar on soil Fe dynamics. We suggest that water management strategies, such as dry-wet cycles, should be employed in rice cultivation to increase Fe2+ oxidation for the inhibition of soil CH4 and CO2 production. Overall, we showed that application of 4 t ha−1 of N-enriched biochar may represent a potential tool to improve sustainable food production and security, while minimizing negative environmental impacts.