© 2019, The Author(s). One of the frontiers in electron scattering is to couple ultrafast temporal resolution with highly localized probes to investigate the role of microstructure on material properties. Here, taking advantage of the high average brightness of our electron source, we demonstrate the generation of ultrafast relativistic electron beams with picometer-scale emittance and their ability to probe nanoscale features on materials with complex microstructures. The electron beam is tightly focused at the sample plane by a custom in-vacuum lens system, and its evolution around the waist is accurately reconstructed. We then use the focused beam to characterize a Ti-6 wt% Al polycrystalline sample by correlating the diffraction and imaging modality, showcasing the capability to locate grain boundaries and map adjacent crystallographic domains with sub-micron precision. This work provides a paradigm for ultrafast electron instrumentation, enabling characterization techniques such as relativistic ultrafast electron nano-diffraction and ultrafast scanning transmission electron microscopy.