The aim of the study was to compare the optimum immobilization conditions of lipase obtained from thermophilic Bacillus aerius and commercial lipase ‘Lipolase’. Both bacterial and commercial lipase were immobilized by surface adsorption onto silica matrix (100-200μm mesh with pore size 2.4 nm) and subsequently exposed to 4% glutaraldehyde, showed binding efficiency of 96.25% and 75.64%, respectively. Maximum enzyme loading was attained after 2 h of incubation in each case. Comparison of various independent variables like reaction time, temperature, substrate affinity, substrate concentration, buffer pH, reusability and thermostability was done to study the effect of matrix on the activity of both bacterial and commercial lipase. Bacterial lipase showed maximum activity with para-Nitrophenyl palmitate (20 mM) at pH 9.5, incubation time of 10 min at 55°C. On the other hand, commercial enzyme showed maximum activity with para-Nitrophenyl palmitate (20 mM) at pH 8.5, incubation time of 10 min and at temperature 40°C. All the metal ions studied exert an inhibitory effect on both bacterial and commercial lipase.