A comparative study on the effect of elevated CO2 environment on soil nitrogen availability in different rice planting system is needed to develop nutrient management strategies in future climate scenarios. A field experiment was conducted inside open top chambers (OTC) to study the effect of elevated CO2 environment with varying nitrogen management on soil NH4+–N and NO3−–N status in two planting system of rice, direct-seeded rice (DSR) and puddled transplanted rice (PTR). The nitrogen management included chemical fertilizer (CF) at 100% (CF100) and 150% (CF150) of the recommended dose, integrated nitrogen management including organic fertilizer (OF) and CF as CF75+ OF75, and site-specific N management through CF using SPAD meter. The soil NH4+–N content was higher in PTR, but NO3−–N was higher in DSR. The soil NH4+–N and NO3−–N content decreased significantly under elevated CO2 environment as compared to ambient in both planting system, except the NO3−–N content at flowering in DSR. The decrease was around 8% for NH4+–N and 5% for NO3−–N content. Soil nitrogen content in DSR can be maintained by following integrated nutrient management (CF75 + OF75) and SPAD-based nitrogen management for sustainable yield. Grain yield, in general, increased with CO2 elevation in both planting system. Under ambient environment, CF150 increased the grain yield by 23% as compared to CF100 in DSR, but no change was noted in PTR. However, under elevated CO2 environment, CF150 increased the grain yield by 13% in PTR. Under elevated CO2 environment, the yield increase of the hybrid rice to additional N fertilizer application was noted in PTR but not in DSR. This study suggests that for sustainable rice production under increasing CO2 environment in future climate scenarios, higher dose of N fertilizer is recommended in PTR, but normal dose in DSR production system.