Plant factories have been developed to replace traditional agriculture, aiming to solve future problems of food availability. However, the nutrient solution in a plant factory is discharged after a single batch of plant cultivation, giving rise to large amounts of waste nutrient solution. Microalgae can be used to treat a wide variety of wastewater and effectively remove excessive nutrients from wastewater. Therefore, the incorporation of microalgal cultivation into a plant factory to treat waste nutrients would be a reasonable approach facilitating removal of waste nutrients with concomitant production of algal biomass. In this study, we isolated novel microalgal species suitable for the growth in waste nutrients from a plant factory and subsequently an underwater LED photobioreactor was constructed being incorporated into the plant factory system. Finally, treated waste nutrient solution was recycled back into the plant factory and successfully used for the cultivation of plant of butterhead lettuce (Lactuca sativa L.).