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In the present research, an alternative eco-efficient biotechnology system, both selective and environmentally viable, is proposed and compared to a conventional scheme. The results showed an optimal process function and a significant difference (<i>p</i> < 0.001) in wastewater measured quality parameters compared to the conventional scheme. Indeed, the treated wastewater from the eco-efficient process revealed significant concentrations of organic matter and nutrients. Accordingly, there was an improvement in soil and plant quality parameters as a result of irrigation with raw urban wastewater and treated wastewater from the eco-efficient system compared to ground water.