Methods and systems for endpoint detection of lyophilization processes are provided. A method for detecting an endpoint in a lyophilization process includes monitoring a total pressure of gases within a chamber containing a sample undergoing lyophilization and controlling a mass rate of flow of inert gas delivered to the chamber to replace water vapor removed from the chamber. The method further includes determining that sufficient water has been removed from the chamber based on total pressure and mass flow rate of inert gas being delivered.