Commercial-scale recycling of agricultural and municipal wastes into organic soil amendments facilitates safe disposal of waste and reduces environmental contamination. However, phytotoxicity of commercial organic amendments to crops is a major concern to farmers. Consistent with this, commercial chicken manure and Milorganite (recycled from municipal waste) were found to be phytotoxic. Chicken manure aqueous extract contains 10.8 ppm Cu and 0.7 ppm Ni. The level of Cu and Ni in Milorganite is lower. The current study identified an aqueous solution containing 5 ppm Cu, lower than in chicken manure aqueous extract, was highly phytotoxic to mustard seeds germination. Therefore, phytotoxicity of chicken manure is in part due to Cu. An aqueous solution containing 1 ppm Ni was not phytotoxic; whereas 0.125 ppm Ni was phytotoxic when 62.5 ppm Na, which is nontoxic, was added to the solution. Therefore, synergistic effects of chemicals in the organic amendments may induce phytotoxicity.