Organic agricultural production systems are favored as they avoid the soil, air, and water contamination. Cow and poultry manure composts are key sources of fertilizer for organic crop production, but their natural degradation is slow that result in the loss of nitrogen. Therefore, the current study aimed to improve the composting process of cow and poultry manures through the addition of effective microorganisms (EM.1), a different exploitation from its normally intended use. Cow and poultry manures, with (CMEM.1 and PMEM.1) and without (CMplain and PMplain) EM.1 were composted and evaluated for organic alfalfa production. Compost analysis indicated superiority of EM.1 compost over plain compost. Significant (p < 0.05) variation between treatment groups was found for most parameters, including plant height, leaf to stem ratio, fresh and dry forage yields, and mineral (N, P, Ca, B, Mn, Fe, Cu, and Zn) composition. Only nodulation and some mineral compositions (K, Mg, S, Na, Co, and Mo) were not significantly different between treatments. Overall superiority of the treatments was in the order of CMEM.1 > CMplain > PMEM.1 > PMplain. We conclude that EM.1 enhances compost quality and alfalfa crop yield. These findings are hoped to encourage sustainable organic alfalfa production and may be applicable to other crops. Furthermore, the article includes analysis for manures, soil, and alfalfa crops that may be useful as reference.