The purpose of this research was to study the effect of two process parameters (temperature and moisture content) on dehydration behavior of different materials using a novel multichamber microscale fluid bed dryer with a process air control unit and in-line near-infrared (NIR) spectroscopy. The materials studied were disodium hydrogen phosphates with three different levels of hydrate water and wet theophylline granules. Measured process parameters of fluid bed drying were logged, including in-line NIR signals. Off-line analyses consisted of X-ray powder diffraction patterns, Fourier transform NIR spectra and moisture contents of studied materials. During fluid bed drying, the stepwise dehydration of materials was observed by the water content difference of inlet and outlet air, the pressure difference over the bed, and the in-line NIR spectroscopy. The off-line analysis confirmed the state of solid materials. The temperature and the moisture content of the process air were demonstrated to be significant factors for the solid-state stability of theophylline. The presented setup is a material and cost-saving approach for studying the influence of different process parameters on dehydration behavior during pharmaceutical processing.