The microwave oven has become a standard appliance to reheat or cook meals in households and convenience stores. However, the main problem of microwave heating is the non-uniform temperature distribution, which may affect food quality and health safety. A three-dimensional mathematical model was developed to simulate the temperature distribution of four ready-to-eat sausages in a plastic package in a stationary versus a rotating microwave oven, and the model was validated experimentally. COMSOL software was applied to predict sausage temperatures at different orientations for the stationary microwave model, whereas COMSOL and COMSOL in combination with MATLAB software were used for a rotating microwave model. A sausage orientation at 135° with the waveguide was similar to that using the rotating microwave model regarding uniform thermal and electric field distributions. Both rotating models provided good agreement between the predicted and actual values and had greater precision than the stationary model. In addition, the computational time using COMSOL in combination with MATLAB was reduced by 60% compared to COMSOL alone. Consequently, the models could assist food producers and associations in designing packaging materials to prevent leakage of the packaging compound, developing new products and applications to improve product heating uniformity, and reducing the cost and time of the research and development stage.