An important component of the pulsed electric field (PEF) technology is the treatment chamber in which the food is exposed to high voltage pulses. Non-uniformity of the treatment, particularly with respect to the electric field distribution, is a common problem in continuous PEF treatment chambers. A previously developed and validated Multiphysics model of a pilot-scale PEF system with co-linear electrode configuration was simplified and embedded into an iterative algorithm, automatically modifying the model's treatment chamber geometry and dimensions, and evaluating the simulated process with respect to a set of performance indicators. The algorithm was capable of identifying configurations that were superior to the standard co-linear treatment chamber configuration. A 3D Multiphysics model with the identified geometrical properties was developed and a corresponding treatment chamber manufactured. The Multiphysics model was validated by comparing measured and predicted temperatures at various process conditions induced in NaCl solution and apple juice. Crown Copyright (C) 2011 Published by Elsevier Ltd. All rights reserved.