Sodium alginate-Chlorella (Na-Alg/Ch) and polypyrrole-Chlorella (PPy/Ch) conjugates were prepared and characterized by SEM, pHPZC and FT-IR techniques. Using de-oiled biomass of Chlorella, the conjugates of Na-Alg/Ch and PPy/Ch were synthesized and employed for the sequestration of Congo Red (CR) dye as a function of various process variables. At optimal conditions of process variables, the PPy/Ch conjugate showed the dye sequestration efficiency of 772.7 mg/g. The maximum CR dye sequestration was achieved at pH 5, dose of the adsorbent 0.05 g, contact time 120 min, 30 °C and 50 mg/L initial concentration of the dye. Also, Chlorella strain was cultivated in municipal wastewater, which reduced the total nitrogen (TN), total phosphorus (PP) and COD (chemical oxygen demand) up to 85.5, 88 and 86.4 (%), respectively. The Freundlich isotherm and pseudo second order kinetics models fitted well to the CR dye adsorption data on to the Na-Alg/Ch and PPy/Ch conjugates. The CR dye sequestration on to Na-Alg/Ch and PPy/Ch was a feasible process and exothermic in nature. Results revealed that PPy/Ch conjugates have promising potential to remove CR dye from the effluents.