Introduction: Rice is the main food crop of the world, and the cultivation of rice crop during the monsoon season is hard due to the rain-induced waterlogging. Apart from this, farmers in north-eastern regions of India often implement improper crop management leading to poor yields. Thus, the development of suitable management practices under improved varieties of rice become essential for increasing rice productivity, improving soil quality status and reducing methane emission. Methods: The aim of the study was to investigate the variation in soil properties, crop growth and methane emission under the application of an inorganic fertiliser as well as its mixtures with both inorganic and plant materials. In such an attempt, a field-based experiment was conducted with the rice variety Chandrama during 2015 in slightly acidic soil having sandy loam texture. Five amendments, i.e. NPK and NPK, blended separately with magnesium sulphate, fresh neem (Azadirechta indica) leaves, used tea (Camellia sinensis var. assamica) leaves, and fresh karanj (Pongamia glabra) leaves were used for the study with four replications each. Results: Application of NPK separately with the leaves of neem, tea and karanj separately at the onset of monsoon season markedly affected the soil porosity and the water-holding capacity of the soil. However, in comparison with sole NPK fertilisation, a significance increase in soil organic matter accumulation (2.48 ± 0.10%) was seen only for karanjblended NPK while magnesium sulphate-blended NPK showed the lowest methane emission (0.30 ± 0.01 mg/m