We investigated methane (CH4) and nitrous oxide (N2O), two important greenhouse gases (GHGs) emissions using the closed chamber method from a flooded rice field in Brahmaputra valley of Assam, northeast part of India. We tried to understand the factors responsible for the emission and identify appropriate agro-technologies for their mitigation. Various factors like water level, drainage management, soil organic carbon management, crop management, fertilizer amendment, cultivar type etc. affect the GHG production and emission from the flooded rice soil. In this study, six treatments were employed, namely, farmer's practice (FP), recommended fertilizer dosage (RDF), direct seeded rice (DSR), intermittent wetting drying (IWD), use of efficient methanotrophs (MTH), and use of ammonium sulfate as a nitrogen source for real-time nitrogen management using leaf color chart, (AS). GHG flux was measured through the static closed chamber technique. Soil temperature, pH, and redox potential (Eh) and other soil physico-chemical and biological properties that have a potential role in GHG emission were also assessed. The lowest CH4 flux was observed in IWD treatment. The highest CH4 but lowest N2O flux was observed in RDF thus portraying a tradeoff relationship among these two GHGs. The highest N2O flux was observed in AS. Changes in Eh strongly altered CH4 and N2O emissions. The CH4 flux for the growing season varied from 62.5 to 86.3 kg ha−1 with an average of 72.4 kg ha−1. The average N2O flux was 0.89 kg ha−1 with values fluctuating between 0.72 – and 1.08 kg ha−1. The findings of this study could assist in understanding the factors affecting the source, production, and sink of these two important GHGs. IWD, along with judicious N-based fertilizer use, could provide significant respite from GHG emissions in rice-based agriculture. These climate-smart strategies not only reduce emissions but also have the potential to improve yield.