The inactivation by high-pressure homogenisation of two microbial strains similar in shape but of different membrane resistance, namely a Gram-negative, Escherichia coli, and a Grampositive bacterium, Lactobacillus delbrueckii, was investigated to clarify the main factors influencing cell inactivation. Tests were carried in a lab-scale Stansted Power Fluid highpressure homogenizer up to 250 MPa and several homogenization cycles. Results exhibited a strong dependence on initial cell concentration, which suggests a cell-cell interaction in the disruption valve enhancing bacterial inactivation to higher extent than in other homogenisation apparatus reported in literature. In addition, a strong difference was found between the two bacterial strains, with the Gram-positive one exhibiting a significantly higher resistance to the treatment. Hence, a treatment was optimised for fruit juices, by determining the optimal operating pressure and number of passes through the homogeniser for achieving the lethal disruption of the bacteria, yet preserving the sensory and nutritional attributes.