Microalgae have the ability to utilize nutrients present in wastewater and generate biomass that is abundant in carbohydrates, lipids, and proteins. The ability of microalgae to integrate wastewater management and biofuel production makes them a promising solution for enhancing environmental sustainability. The objective of this study was to assess the potential of local microalgae, Scenedesmus sp., to simultaneously remediate wastewater and produce lipids. The microalgae were cultivated in anaerobically digested brewery effluent, both sterilized and non-sterilized, to evaluate their phycoremediation and lipid production capabilities. The phycoremediation study was investigated by measuring chemical oxygen demand (COD), total nitrogen (TN), ammonium–nitrogen (NH4+-N), and total phosphorus (TP) removal from brewery effluent. Lipids were extracted from microalgal biomass without and with pretreatment methods, such as microwave, autoclave, osmotic stress, oven heating, and HCl digestion in a water bath, to enhance lipid extraction. Results indicate that Scenedesmus sp. achieves higher biomass production in non-sterilized brewery effluent compared to sterilized brewery effluent. Conversely, it attains higher lipid accumulation in sterilized brewery effluent compared to non-sterilized brewery effluent. Scenedesmus sp. also attained a higher removal of TP (69.32%) and COD (77.78%) in non-sterilized effluent, but TN (96.14%) in sterilized brewery effluent. The removal of NH4+-N was nearly 100% in both effluents. The maximum lipid content obtained was 14.79%, which was enhanced by 39.06%, 23.89%, 15.81%, 11.61%, and 4.78% after microwave, HCl digestion, autoclave, osmotic, and oven heating pretreatments, respectively. The findings of this study demonstrate that local microalgae have a great potential for wastewater remediation with lipid production using appropriate pretreatment methods.