Microwave (MW) heating is a unique approach that, unlike conduction- and convection-based heating, can provide volumetric heating. Complex microstructural changes in food materials occur because of simultaneous heat and mass transfer during drying, significantly affecting food structure and quality. Food properties, drying methods, and other drying parameters all have an impact on the microstructure of food samples, which in turn affects drying kinetics and food quality. However, no study has been undertaken to investigate the development of nano–micro-pores (NM-pores) on the cell walls and their relationship with the moisture migration mechanism. This study presents a novel investigation of the microstructural changes in food during microwave drying, with a focus on the formation of nano–micro-pores (NM-pores) on cell walls and their impact on moisture transport kinetics. The utilized hot air was maintained at a temperature of 70 °C, whereas microwave (MW) power levels of 100 W, 200 W, 300 W, and 400 W were used in microwave drying. The findings of the study indicate that the development of NM-pores occurs only during intermittent microwave drying (IMCD), while the cell wall of the food samples tends to burn or collapse in continuous microwave drying (CMD) due to the high heat generated. Additionally, no NM-pores were observed in the cell wall during convective drying. During IMCD with microwave power ranging from 100 W to 400 W, a range of pore sizes from 0.1 μm to 8.5 μm were observed. Due to the formation of NM-pores and collapses, MW drying takes around 10–20 times less time than convective drying to remove the same quantity of moisture. The effective moisture diffusivity values were found to be the highest in CMD at 4.70 × 10−07m2/s and the lowest in CD at 2.43 × 10−09m2/s. IMCD showed a moderate diffusivity of 2.45 × 10−08m2/s. This study investigates the formation of NM-pores on cell walls during microwave drying and their impact on moisture transport kinetics and establishes correlations between microstructure modifications and moisture migration pathways.