A protease-secreting bacteria was used to pretreat municipal sewage sludge to enhance aerobic digestion. To enhance the accessibility of the sludge to the enzyme, extracellular polymeric substances were removed using citric acid thereby removing the flocs in the sludge. The conditions for the bacterial pretreatment were optimized using response surface methodology. The results of the bacterial pretreatment indicated that the suspended solids reduction was 18% in sludge treated with citric acid and 10% in sludge not treated with citric acid whereas in raw sludge, suspended solids reduction was 5.3%. Solubilization was 10.9% in the sludge with extracellular polymeric substances removed in contrast to that of the sludge with extracellular polymeric substances, which was 7.2%, and that of the raw sludge, which was just 4.8%. The suspended solids reduction in the aerobic reactor containing pretreated sludge was 52.4% whereas that in the control reactor was 15.3%. Thus, pretreatment with the protease-secreting bacteria after the removal of extracellular polymeric substances is a cost-effective and environmentally friendly method.