Pulsed electric fields (PEF) are an emerging non-thermal treatment valid for liquid foods. This novel technology offers a relevant alternative to traditional thermal methods avoiding thermal damage to the product (loss of flavour and nutritional value). The aim of this work was to evaluate the influence of PEF treatment conditions, inoculum size (initial cell concentration) and substrate conditions after PEF treatment on the inactivation and potential growth of Lactobacillus plantarum and Escherichia coli in orange–carrot juice. Although a maximum inactivation of 1.3 and 2.6 log reductions were achieved for L. plantarum and E. coli, respectively, after PEF treatment, it was effective inducing sub-lethal injury. An increase in the lag-phase duration was evidenced under refrigeration conditions. When sub-lethal damage could be repaired, the subsequent growth rate was not affected. An increased inhibitory effect of PEF, low temperature and low inoculum size on the delay in lag phase was observed.