Crop residue incorporation to the soil is an essential strategy to improve soil quality and crop productivity in order to attain sustainable development goals. Experiments were conducted to evaluate the differential effect of crop residues on CH4 production and consumption in a tropical vertisol. Soils were incubated with residues of cereals (maize and wheat) and legumes (chickpea and soybean) at 1% w/w, under non-flooded and flooded conditions to estimate CH4 consumption and CH4 production rates, respectively. Rates of CH4 production (ng CH4 produced g/soil/day) varied from 0.068 to 0.107 with lowest in chickpea residue and highest in wheat straw amended soil. CH4 consumption rates (ng CH4 consumed g/soil/day) was highest (0.79) in wheat straw amended soil and lowest (0.53) in chickpea residue amended soil. Organic carbon (%) and available NO3− (mM) contents increased significantly (P > 0.05) in residue amended soils over control under both flooded (methanogenic) and non-flooded (methane consuming) conditions. Abundance of methanogens and methanotrophs was estimated as mcr and pmoA gene copies g−1 soil, indicated that both the microbial groups were stimulated significantly due to the amendment of crop residues. Linear models exhibited significant correlation among CH4 production and consumption with organic carbon, available nitrate and microbial abundance. The study highlights that crop residues incorporation influences both CH4 consumption and production potential of soil and this effect is more pronounced with biomass of cereals than legumes.