Meat production is associated with the generation of huge quantities of meat processing wastewater (MPWW) which has high concentrations of nutrients. The utilization of Scenedesmus sp. in the phycoremediation process to treat MPWW has attracted growing interest, but there is inadequate information on the management of biomass of this microorganism. This study aims to optimize the harvesting of Scenedesmus sp. biomass generated during phycoremediation through flocculation with alum and its potential biomass by-product. The removal rates of the chemical oxygen demand, ammonia, total nitrogen, total phosphorus and orthophosphate were 99.16% (R 2 = 0.95), 97.19% (R 2 = 0.91), 93.91% (R 2 = 0.96), 97.25% (R 2 = 0.85) and 99.38% (R 2 = 0.9517), respectively. From the result, the best coagulant for recovery efficiency (97.54%) was recorded at pH 8.6 with 116.85 mg L −1 alum. Three major chemical compoundstetradecanoic, oleic and dodecanoic acidswere recorded in the extraction of Scenedesmus sp. biomass (as determined by gas chromatography-mass spectrometry analysis; these have the potential for use in the cosmetic and medical industries. The main functional groups in the harvested biomass were OH, CH, CO -C and CH CH. It can be concluded that the flocculation method was the most efficient compared to filtration process for recovering Scenedesmus sp. biomass owing to the absence of toxic by-products.