This pot study investigated the effect of the combined application of two commercial biofertilizers viz. Biopower and EM (Effective Microorganisms) on rice (Oryza sativa L.) growth and yield in soils amended with farmyard manure, green manure, and NPK fertilizers. Biopower is a product of the Nuclear Institute for Biotechnology and Genetic Engineering (NIBGE), Pakistan, which contains species of associative and endophytic diazotrophs. EM (effective microorganisms), a product developed by Japanese scientists, consists of co-existing beneficial microorganisms, mainly species of photosynthetic and lactic acid bacteria, as well as yeast. Applying Biopower adversely affected plant growth and yield in NPK fertilizer amendment. Conversely, this biofertilizer markedly enhanced plant growth and yield in green manure amended soil while its effect was not significant in farmyard manure amendment. In green manure amendment, applying EM enhanced grain yield by 46%. Co-inoculation of Biopower and EM evidently improved root and shoot growth in farmyard manure amended soil. This study concludes that the two biofertilizers clearly enhanced shoot biomass and grain yield in green manure amended soils.