The impact of climate change on methane (CH4) emissions from rice production systems in the Coimbatore region (Tamil Nadu, India) was studied by leveraging field experiments across two main treatments and four sub-treatments in a split-plot design. Utilizing the closed-chamber method for gas collection and gas chromatography analysis, this study identified significant differences in CH4 emissions between conventional cultivation methods and the system of rice intensification (henceforth SRI). Over two growing seasons, conventional cultivation methods reported higher CH4 emissions (range: from 36.9 to 59.3 kg CH4 ha−1 season−1) compared with SRI (range: from 2.2 to 12.8 kg CH4 ha−1 season−1). Experimental data were subsequently used to guide parametrization and validation of the DeNitrification–DeComposition (DNDC) model. The validation of the model showed good agreement between the measured and modeled data, as denoted by the statistical tests performed, which included CRM (0.09), D-index (0.99), RMSE (7.16), EF (0.96), and R2 (0.92). The validated model was then used to develop future CH4 emissions projections under various shared socio-economic pathways (henceforth SSPs) for the mid- (2021–2050) and late (2051–2080) century. The analysis revealed a potential increase in CH4 emissions for the simulated scenarios, which was dependent on specific soil and irrigation management practices. Conventional cultivation produced the highest CH4 emissions, but it was shown that they could be reduced if the current practice was replaced by minimal flooding or through irrigation with alternating wetting and drying cycles. Emissions were predicted to rise until SSP 370, with a marginal increase in SSP 585 thereafter. The findings of this work underscored an urgency to develop climate-smart location-specific mitigation strategies focused on simultaneously improving current water and nutrient management practices. The use of methanotrophs to reduce CH4 production from rice systems should be considered in future work. This research also highlighted the critical interaction that exists between agricultural practices and climate change, and emphasized the need to implement adaptive crop management strategies that can sustain productivity and mitigate the environmental impacts of rice-based systems in southern India.