In this research, the effect of intermittent microwave drying (IMD) on drying time and quality characteristics for three varieties of Iranian pistachio nuts was investigated and compared with the sun drying method. The quality parameters, such as chemical characteristics, physical parameters, and sensory evaluation were considered. Three varieties, Kal-Khandan, Kaleh-Bozi, and Ghermez, were dried in an 800-W, 2,450-MHz domestic microwave oven. Experiments were conducted in three material loads of 50, 100, and 150 g under intermittent method at 6 s of power-on and 70 s of power-off with three replications. The total drying time was in the range of 114.03–266.07 min, depending on material loads and varieties. The higher the material load, the longer the drying time. The results showed that the effect of drying method on the shell splitting size was very significant (p < 0.01). Texture analysis showed that the firmness and Meyer hardness of sun-dried pistachio nuts’ kernels are lower than those dried by the IMD method. In IMD by increasing the material loads, the Meyer hardness mean value is decreased. The analysis of chemical characteristics indicated that the IMD has no substantial consequence on sample fat and protein contents, while acidity and peroxide values were affected significantly (p < 0.05). Sensory evaluations revealed that the highest average score was gained at the material load of 150 g.