A microwave based system was developed for drying of apple slices while on-line controlling their temperatures. An infrared thermography assisted control system allowed to realize temperature control by detecting the instantaneous maximum temperature among the samples under test instead of a chosen slice. The effectiveness of the system at hand in realizing temperature control both in space and in time was proven for three temperatures: 55, 65 and 75 degrees C. Temperature fluctuations became larger both with time increasing and with rising temperature levels thus causing a negative impact on dried fruit quality. In fact apples slices dried at 75 degrees C by microwave showed I. (lightness) and white index (WI) values significantly lower (p < 0.05), when compared to the fresh samples and to the apples dried by hot air. To overcome such behaviour a mode stirrer was introduced resulting in halving the temperature spatial oscillations of sample slices. (C) 2012 Elsevier Ltd. All rights reserved.