The effect of concentrated microwave field (CMF) and pulsed electric field (PEF) treatments on inactivation of selected bacteria, yeast and mould in liquid food was investigated. It was concluded that the both unconventional non thermal methods significantly inactivate inoculated microorganism in egg white, liquid whole egg, milk and strawberry juice. PEF method had greater preservation effectiveness (maximum inactivation of 6.5 D for Escherichia coli in strawberry juice) than CMF method (maximum inactivation of 2.7 D for Candida tropicalis in strawberry juice). Optimalization of CMF and PEF parameters was conducted with use of Response Surface Methodology (RSM). The maximum inactivation of microorganism for RSM model in egg products (i.e. egg white and liquid whole egg) was in range 1.02-1.97D for CMF method. Effectiveness of PEF method in RSM model was higher: 3.77D for liquid whole egg and 3.82D for milk. Obtained results in our studies confirm that non thermal methods like PEF or CMF significantly reduce microflora in liquid food systems.