The aim of this research was to analyze greenhouse gas (GHG) emission in paddy rice–based cropping systems of the Middle Indo–Gangetic plains in India. Two paddy rice–based systems, namely paddy rice–wheat (PW) and paddy rice–potato–fallow (PP), were studied for GHG emission, net return (NR) and eco–efficiencies (EE). The PW (3354.9 ​± ​133.7 kgCO2eq ha−1 y−1) and PP (5096.3 ​± ​11.6 kgCO2eq ha−1 y−1) systems were observed to have significantly different GHG emissions. The most significant contributor to the GHG pool was fertilizer production, contributing about 40.3% and 46.1% in the PW and PP systems, respectively. On–farm direct nitrous oxide (N2O) emission was the second largest contributor to the GHG emission pool. Farm sizes significantly affected GHG emissions in the PW system, and medium farms (>3 ​ha) had higher GHG emission compared to other farm sizes. While the NR in the PP system was significantly higher (2504.3 ​± ​65.6 USD ha−1 y−1) compared to the PW system (1687.1 ​± ​90.6 USD ha−1 y−1) owing to better market prices of potato crop, it also performed slightly better on the EE scale (0.52 and 0.50 USD kgCO2 eq−1, respectively). In the PW system, comparatively larger farms were more eco–efficient than the smaller farms. However, the EE values for different farm sizes in the PP system were numerically and statistically similar. The results reported in this study may be beneficial to farmers to make decisions pertinent to sustainable management of agro inputs in paddy–based cropping systems and collective farming. Moreover, these results can even be utilized by governmental and non–governmental organizations for deciding support/subsidies to farmers in the study area.

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