This study evaluates the efficiency of the inactivation of Escherichia coli K12, entrapped within calcium alginate gel, by microwave processing compared to a conventional approach i.e. by heating in a water bath. Microbial thermal inactivation equations coupled with heat transfer and Maxwell's equations are integrated into a 3D Finite Elements model under dynamic heating conditions. Water bath microbial inactivation experimental data are exploited for performing parameter identification of a non-linear microbial model, and the Calcium alginate gel's dielectric properties were numerically estimated. The coupled model provides a very good fitting to the experimental results. The simulation have shown uneven temperature distribution during microwave heating which may interpret its lower inactivation efficiency comparing to the conventional water bath treatment. This study also demonstrates the reliability of the coupled modeling approach to estimate the efficiency of the microbial inactivation, despite the thermal heterogeneity inherent in the microwave treatment. (C) 2012 Elsevier Ltd. All rights reserved.