A continuous lab-scale integrated bio-system was conducted to treat sewage wastewater from Abu-Rawash wastewater treatment plant (WWTP). The bio-system showed high efficiency in removing chemical oxygen demand (COD), biological oxygen demand (BOD5), and total suspended solids (TSS). The experimental analysis results indicated that the maximum COD removal and methane yields were 97.6 and 13.74 mmol CH4/Kg COD at a hydraulic retention time (HRT) of 6 h, respectively. Zn, Mn, and Fe were removed at a high rate of up to 96.6%. The sponge bio-carriers have improved overall treatment performance and substantially improved mixed liquor volatile suspended solids/mixed liquor suspended solids (MLVSS/MLSS) ratio at an appreciated range, and the total pathogenic organisms were removed up to 99.8% in the second stage. Because the innovative bio-system enables a rapid startup process, is simple to use, and is inexpensive, it can provide an economically feasible alternative for wastewater management and could be extended to full-scale applications for agricultural purposes.