Materials modelling and processing require experiments to visualize and quantify how external excitations drive the evolution of deep subsurface structure and defects that determine properties. Today, 3D movies with ~100-nm resolution of crystalline structure are regularly acquired in minutes to hours using X-ray diffraction based imaging. We present an X-ray microscope that improves this time resolution to <100 femtoseconds, with images attainable even from a single X-ray pulse. Using this, we resolve the propagation of 18-km/s acoustic waves in mm-sized diamond crystals, and demonstrate how mechanical energy thermalizes from picosecond to microsecond timescales. Our approach unlocks a vast range of new experiments of materials phenomena with intricate structural dynamics at ultrafast timescales.