The drying behavior of (S)-N-acetylindoline-2-carboxylic acid, precipitated (1a, 17 wt %) and nonprecipitated (1b, 5 wt %), and N-acetyl-(S)-phenylalanine ((S)-2-acetamido-3-phenylpropanoic acid, 2), both pharmaceutical intermediates, and of cocarboxylase hydrochloride (thiamine pyrophosphate, 3), a coenzyme, a bioactive form of vitamin B1, being a thermolabile substance, has been determined in straightforward drying setups. The method of supplying energy to the system had a profound influence on the drying rate and on the internal temperature of the samples during drying. The drying time of (S)-N-acetylindoline-2-carboxylic acid (1b) with the low moisture content (5 wt %) could be reduced by a factor 4 using microwave irradiation instead of conventional heating, while keeping the sample temperature under 35 °C. N-Acetyl-(S)-phenylalanine (2) with a higher moisture content (22 wt %) demonstrated a decrease in drying time by a factor 2.5 to 4 depending on the applied microwave powers. A reduction in drying time of the precipitated (S)-N-acetylindoline-2-carboxylic acid (1a, 17 wt % moisture) by a factor 2 was demonstrated for drying at 150 W of microwave irradiation instead of using a water bath at 70 °C. A dramatically shorter drying time by a factor 10 was found for cocarboxylase hydrochloride (3, 15 wt % water) on lab-scale which could be reproduced on pilot-plant scale. To achieve with conventional heating similar drying times as under microwave irradiation for the four examples, extremely high energy inputs should be applied, necessitating extremely high temperature differences between the heating source and the sample. The results reveal that microwave irradiation is less energy-consuming and is particularly useful for effective drying of thermally unstable materials in short periods of time.