Microbial and enzyme inactivation by pulsed electric field (PEF) treatment was assessed in a blended plant-based milk alternative (PBMA) containing oats and pea protein without the application of presterilization. This was conducted to investigate a novel approach that permits PEF process validation for PBMA containing heat-labile components (protein and starch). Continuous PEF processing at moderate field strengths (9–10 kV/cm) combined with mild preheating (30–45 °C) for 25 s was applied over a range of specific energy inputs (77–245 kJ/L). Selective plating permitted bacterial enumeration of inoculated surrogate organisms, despite the presence of natural microbial contaminants in the non-presterilized product. A minimum 5-log reduction of inoculated surrogates Escherichia coli and Listeria innocua alongside native microbiota was identified after preheating to 35–45 °C followed by PEF at 192–215 kJ/L. α-amylase activity was reduced by up to 89% during a similar PEF treatment (205 kJ/L, 40 °C preheating). Overall, continuous PEF combined with mild preheating temperature was shown to achieve microbial inactivation in the pea protein enriched PBMA in compliance with current food safety regulations. Industrial relevancePresterilization is typically applied prior to conducting microbial challenge testing on food products to validate novel pasteurization treatments according to current regulatory requirements that a minimum 5-log reduction of relevant inoculated food pathogens must be achievable. However, for a variety of blended PBMA containing heat-labile proteins, presterilization is not advisable as the occurrence of irreversible changes in the product quality linked to protein coagulation and phase separation will affect the inactivation efficacy during subsequent microbial challenge testing. Hence, an alternative approach is presented utilizing a non-presterilized PBMA and thorough microbiological analysis, combining non-selective and selective plating techniques. This allows an identification of PEF treatment parameter with a minimum 5-log reduction of inoculated surrogate organisms alongside naturally present microbial contaminants. This may serve as a valuable guideline for stakeholders in the food industry when addressing the efficacy of novel preservation treatments such as PEF in PBMA products with similar heat-induced product stability challenges.