Solar-powered membrane distillation is a promising technology for water desalination, especially in remote arid areas. However, the intermittent nature of solar irradiation restricts the operation of this technology to the daylight hours. Many studies tried to extend the daily operating period but at the expense of increasing complexity and cost. Therefore, most likely the stand-alone solar-powered system will be operated intermittently. This work is focused on studying the effect of the intermittent operation on a solar-powered MD system performance. A set of experiments were carried out on a bench-scale membrane distillation unit. A programmable temperature-controlled circulating bath was used to generate a feed temperature pattern similar to the temperature output of a solar heater in a real pilot solar-powered system. Different operation shutdown procedures (protocols) were examined to identify the best operation protocol for intermittent operation of MD system. The results showed fluctuations in the daily permeate flux and quality. Moreover, the permeate flux was observed to increase with the thermal expansion of the membrane material. There was a gradual deterioration in membrane module performance in terms of salt rejection when the module left to dry overnight. On the other hand, keeping the saline feed inside the module overnight was found to preserve the performance of the module. Ultrasonic cleaning was applied to the used hollow fiber membranes and found to help in recovering their hydrophobicity. This is observed by an increase in the contact angle values of these membranes from 77 degrees to 98 degrees.