One way of making livestock farming a more sustainable practice is to raise cattle organically. However, regardless of the production system, there is a generation of residues that can be converted into energy resources using biodigesters. This study aimed to evaluate the addition of inoculum in the anaerobic biodigestion of cattle manure under organic (OPS) and conventional production systems (CPS) in an Indian model biodigester. The physicochemical (pH, EC, TS, VS, DBO, and COD) and microbiological characteristics of the affluent and effluent, as well as the production, potential, and qualitative characteristics of the biogas, were evaluated. CPS showed higher reductions in TS, VS, BOD, and COD than OPS, with the highest effect of biogas production. Regarding the effect of inoculum addition, the treatment with 20% inoculum provided in both production systems high acceleration at the starting point of biogas production and increased energy potential, as well as high reductions in VS, BOD, and COD. Thus, there is a need to use 20% inoculum for high biogas productivity, regardless of the production system.