This research explores the two-phase flow behavior involved in enhanced dense phase carbon dioxide inactivation of E. coli DH5α, which has been shown to possess a high microbial reduction efficiency of up to 3.7 ± 0.4 log. We present an experiment in which the liquid sample was pressurized with liquid carbon dioxide to 8.2 MPa and, after saturation, was forced to flow through a mini tube. An experimental setup was developed to visualize the flow patterns (plug, slug and churn flows) occurring in the mini tube by means of high-speed imaging. The values of the wall shear stress were estimated within the mini tube with the help of the gas slug velocities (8–9 m/s) and were compared with threshold shear stress values reported for the disruption of fresh E. coli cells. The results suggest that the preliminary pressurization phase may cause a substantial destabilization of the cell wall of E. coli DH5α.