Thermal process optimization has focused on traditional sterilization, with limited research on pasteurization or microwave-assisted thermal processing. Model foods have been developed as quality evaluation tools for thermal pasteurization processes, but there are no comprehensive studies demonstrating how these model foods could be used to evaluate and compare the resulting food quality after different pasteurization processes. The aim of this study was to develop a methodology using image and quantitative analyses for quality evaluation of pre-packaged food pasteurized using a microwave-assisted pasteurization system (MAPS) and traditional hot water method. Four pasteurization processes (MAPS and hot water method at 90 and 95 °C) were designed to have an equivalent accumulated thermal lethality at the cold spot of at least 90 °C for 10 min to control nonproteolytic Clostridium botulinum spores. Color-based time-temperature indicators in mashed potato and green pea model foods were quantified using image analysis. Results showed that median color values were useful in assessing overall color change, and interquartile range was an indicator of burnt areas. MAPS 95 °C was the best process because it had the smallest hot spot cook values and the least color change, while the 90 °C hot water process was the worst. Model foods and image analysis techniques were useful pasteurization process quality evaluation tools and made it possible to visualize the potential food quality change volumetrically, throughout a food package. In the future, these tools could be combined with computer simulations to optimize the quality of pilot-scale and industrial MAPS or conventional pasteurization processes.