Microwave and ohmic heating are becoming a more popular choice for heating in aseptic processing due to rapid heating for bacteriological destruction and better product quality. Due to regulatory constraints and the complexities of validation requirements, the food industry has been struggling to launch aseptic low-acid products containing particles into the market with confidence. This study aims to find an alternative approach to simulate and mimic processing conditions by modeling and validating the model process by using surrogate particles and microorganisms. A mathematical model was used to simulate the heat transfer in the carrier fluid and solid particles. For the validation of the process, a simulated particle was designed to create the worst-case conditions, being both the fastest moving and slowest heating compared to the real food particles. These particles with conservative thermal and physical properties were inoculated with Geobacillus stearothermophilus spores as a surrogate microorganism for the microbiological validation of the thermal process. Magnetic implants were embedded in simulated spherical particles (12.77 mm and 15.88 mm) to measure the residence time distribution. Total accumulated lethality using the surrogate system was estimated at F0 > 7.7 min. The microwave aseptic system was microbiologically validated to produce shelf-stable particulate food products.