Shell and Tube Heat Exchanger (STHE) is a commonly used type of heat exchanger in various industries due to its cost-effectiveness and ease of maintenance. Continuous washing and maintenance of STHE play an important role in influencing both the quality and quantity of production from biodiesel plants. In this particular investigation, the STHE serves as a cooling medium for biodiesel production, with cooling water circulating on the tube side and biodiesel flowing on the shell side. This study focuses on removing silica crust buildup caused by cooling water in the STHE. Furthermore, a Clean-in-Place machine and a 10% citric acid solution with variable washing times of 2, 4, 6, 8, 10, and 12 hours were used for the cleaning process. The results indicate a significant 250% increase in the volumetric flow rate of the cooling tower along with an increase in the overall Heat Transfer Coefficient after 10 hours of washing. Further analysis at the hours mark showed consistent results, suggesting a steady state. Beyond this point, no additional temperature decrease was observed, with temperature stabilizing at 32oC. The results of the Scanning Electron Microscope show that the crust formed in the STHE comes from silica found in cooling water.