Solid-phase epitaxy (SPE) and other three-dimensional epitaxial crystallization processes pose challenging structural and chemical characterization problems. The concentration of defects, the spatial distribution of elastic strain, and the chemical state of ions each vary with nanoscale characteristic length scales and depend sensitively on the gas environment and elastic boundary conditions during growth. The lateral or three-dimensional propagation of crystalline interfaces in SPE has nanoscale or submicrometer characteristic distances during typical crystallization times. An in situ synchrotron hard x-ray instrument allows these features to be studied during deposition and crystallization using diffraction, resonant scattering, nanobeam and coherent diffraction imaging, and reflectivity. The instrument incorporates a compact deposition system allowing the use of short-working-distance x-ray focusing optics. Layers are deposited using radio-frequency magnetron sputtering and evaporation sources. The deposition system provides control of the gas atmosphere and sample temperature. The sample is positioned using a stable mechanical design to minimize vibration and drift and employs precise translation stages to enable nanobeam experiments. Results of in situ x-ray characterization of the amorphous thin film deposition process for a SrTiO3/BaTiO3 multilayer illustrate implementation of this instrument.