This study explores the potential of strain selection and adaptation for developing a fungi-yeast-microalgae consortium capable of integrated bioethanol production and livestock wastewater treatment. We employed a multi-stage approach involving isolation and strain selection/adaptation of these consortiums. The study started with screening some isolated fungi to grow on the cellulosic biomass of the livestock wastewater (saccharification) followed by a fermentation process using yeast for bioethanol production. The results revealed that Penicillium chrysogenum (Cla) and Saccharomyces cerevisiae (Sc) produced a remarkable 99.32 ppm of bioethanol and a concentration of glucose measuring 0.56 mg ml− 1. Following the impact of fungi and yeast, we diluted the livestock wastewater using distilled water and subsequently inoculated Nile River microalgae into the wastewater. The findings demonstrated that Chlorella vulgaris emerged as the dominant species in the microalgal community. Particularly, the growth rate reached its peak at a 5% organic load (0.105385), indicating that this concentration provided the most favorable conditions for the flourishing of microalgae. The results demonstrated the effectiveness of the microalgal treatment in removing the remaining nutrients and organic load, achieving a 92.5% reduction in ammonia, a 94.1% reduction in nitrate, and complete removal of phosphate (100%). The algal treatment also showed remarkable reductions in COD (96.5%) and BOD (96.1%). These findings underscore the potential of fungi, yeast, and Nile River microalgae in the growth and impact on livestock wastewater, with the additional benefit of bioethanol production.Graphical abstract