The study of sophisticated biomaterials and their cellular targets requires visualization methods with exquisite spatial and temporal resolution to discern cell organelles and molecular events. Monitoring cell-material interactions at high resolution is key for the continued development and optimization of biomaterials, for monitoring cell uptake of cargo, and for understanding the cell response to extracellular cues. This review evaluates the advantages and disadvantages of different forms of electron microscopy and super-resolution microscopy in elucidating how biomaterial surface chemistry and topography can affect intracellular events at the nanoscale.