Continuous production processes and an adequate supply of raw materials are necessary to satisfy the growing demand for biodiesel. The use of different feed oils could be necessary to ensure sufficient supply for biodiesel production in certain circumstances; however, changing feed oil during the operation of a continuous reactor causes process disturbances. The present study analyses the effect of feed oil changes on the continuous operation of a industrial continuous stirred-tank reactor (CSTR) using a model which takes the dynamics of oil changes into account. The models previously reported only consider the operation of reactor with only one vegetable oil. The model in this work was developed by mass and energy balances. A methodology to model oil changes is presented. Glycerides and esters were characterized using adequate approaches. Moreover, accurate methods for predicting essential properties in the biodiesel manufacturing were used for the estimation of their thermo-physical properties. The kinetic parameters of the transesterifications were calculated from consistent studies selected from an exhaustive literature revision. The results show that temperature is practically not affected after oil changes; however, the ester concentration varies considerably. The ester mass fraction varying by up to 22.07% after an disturbance.