Microalgae possess many advantages, but the lack of a suitable strategy to simultaneously facilitate their low cost cultivation and high value productions limits their commercial applications. In this study, two microalgae strains (RT_C and RT_F) isolated from a municipal wastewater treatment plant were used to establish a two-step wastewater treatment process. During step-1, RT_C was cultivated in composite wastewater due to its high tolerance of sludge centrate; followed by step-2, in which the supernatant generated from RT_C culture was used to cultivate RT_F. The NH4+-N, PO43--P, and COD in the wastewater were removed almost completely using this strategy. Moreover, the majority of the metal ions in the wastewater were absorbed by RT_C during step-1, and thus the powdered RT_F only contained low levels of toxic metals. Our results demonstrate that this two-step process is effective for removing pollutants and while generating a powder sufficiently clean for extracting valuable compounds.