Significance Despite the increasing efforts in developing affinity grids to facilitate sample preparation for challenging systems and dynamic complexes, they are not widely used in cryo-electron microscopy (EM) owing to concerns of limiting resolution. We show that our affinity grids extract proteins through covalent bonding with 3.3-Å reconstruction. To our knowledge, no example of small proteins (<200 KDa) has been successfully tested with other affinity grids. With encouraging results further from a mixture sample, we believe that the strategy described here is highly applicable to a broad array of challenging macromolecules and thus is a method of broad interest to the cryo-EM community. The dramatic improvement in cryo-EM sample preparation outlined here paves the way to “purification on the grid.”