A method for detecting in real time structure changes of a food product during a heat transfer process in an agitated vessel is proposed. The method is based on electrical conductivity measurements and a modified Generalized Likelihood Ratio (GLR) algorithm was applied to the first derivative of the electrical conductivity signal. The paper describes in details protocol for carrying out such method. Examples of structure changes obtained for a starch mixture and a gelatin solution are presented. Finally, by monitoring apparent viscosity of the solution during heating, reliability of change detection in real time is ascertained.