The growing human population and scarcity of arable land necessitate agriculture intensification to meet the global food demand. Intensification of agricultural land entails manure input into agrosystems which have been associated to increased methane emission. We investigated the immediate short-term response of methane production and the methanogens after manure amendments in agricultural soils and determined the relevance of the manure-derived methanogenic population in its contribution to soil methane production. We followed methane production in a series of unamended and manure-amended batch incubations: (i) manure and soil, (ii) sterilized manure and soil, and (iii) manure and sterilized soil. Moreover, we determined the methanogenic abundance using a quantitative PCR targeting the mcrA gene. Results show that the soil-borne methanogenic community was significantly stimulated by manure amendment, resulting in increased methane production and mcrA gene abundance; manure-derived methanogenic activity contributed only marginally to overall methane production. Accordingly, our results highlighted the importance of the resident methanogenic community and physiochemical properties of a residue when considering methane mitigation strategies in agricultural soils.