The evaluation of cell disruption efficiency is important in monitoring durability and diverse cellular physiologies of host cells and improving recovery yield of intracellular products. On the basis of our previously suggested pH-controlled fluorescence resonance energy transfer (FRET) system, we herein demonstrated that easy and effective estimation of the degree of cell disruption under certain stress environments is possible using a simple measurement of changes in fluorescence spectra of two fused fluorescent proteins, because its unique linear correlation was established with cell disruption efficiency from the conventional colony counting method.