Ammonia contamination from fertilizer production, palm oil processing, livestock, and food industries is a major contributor to eutrophication, aquatic toxicity, and ecosystem degradation. Conventional treatment methods often struggle with high ammonia concentrations, prompting interest in biological approaches. One promising solution is the use of immobilized microalgal–bacterial beads (IMBB), which combine microbial synergy with enhanced stability and reusability. Building on this approach, this study optimized ammonia removal and developed an empirical predictive model using IMBB, while characterizing their physicochemical properties through SEM–EDS, FTIR, and mechanical strength analysis. Three independent variables—ammonia concentration (250–500 mg L⁻¹), bead dosage (20–40 g L⁻¹), and bead size (3–7 mm)—were evaluated via Response Surface Methodology (RSM). Optimal conditions were identified at 422.65 mg L⁻¹ ammonia, 37.88 g L⁻¹ beads, and 7 mm bead size, achieving a predicted removal efficiency of 93.83%. SEM revealed a dense and uniform bead structure; EDS detected C, O, Na, and Ca as dominant elements; and FTIR confirmed O–H, COO⁻, and C–O–C functional groups. Mechanical testing showed a strength reduction from 136.30 to 7.62 gForce post-operation. These findings demonstrate the potential of IMBB as a robust, sustainable biotechnology for efficient ammonia removal in industrial wastewater treatment.