Abstract A comprehensive 3D, transient-free convection, and multiphase model was developed to determine the performance of ohmic heating (150, 200 and 250 V; 120 s; 99.4 °C) and conventional heating (90 °C; 15 min) for the inactivation of Escherichia coli, Staphylococcus aureus, Salmonella enterica subsp. enterica serovar Paratyphi A, Salmonella Typhi, Shigella dysenteriae, and Shigella flexneri in blended citrus juice (sweet lemon and orange). Results indicated the computed temperatures were in good agreement with the experimentally measured data (below 5% deviation). The examination of velocity and temperature patterns throughout the computational domain explained the reasons for significant differences between the conventional and ohmic heating process. The homogeneously distributed vortices in ohmic heating lead to a more uniform and rapid temperature rise in temperature (from 26 to 99.4 °C) while compared with the conventional method with a stratified flow pattern. Based on the evaluation of temperature rise, increasing in the applied voltage from 150 to 250 V was deducted to reduce the inactivation time about 20–30% for the investigated pathogens. The inactivation rate of pathogens during ohmic heating process was maximum for S. aureus, followed by E. coli, S. enterica subsp. enterica serovar Paratyphi A, S. Typhi, S. dysenteriae and S. flexneri. In conclusion, the developed numerical modeling can be conveniently applied to simulate and predict the ohmic heating for the inactivation of pathogenic bacteria. Industrial relevance Several thermophysical phenomena affect the optimization and design of ohmic heating systems such as heat and mass transport as well as electrical field distribution. The implementation of the computational fluid dynamics (CFD) method is an efficient and economical technique that can provide valuable data for researchers. Moreover, the determination of off-design thermal spots, heat-loss magnitude and apparatus efficiency can be determined via numerical calculations.