Intercalation materials are promising candidates for reversible energy storage and are, for example, used as lithium-battery electrodes, hydrogen-storage compounds, and electrochromic materials. An important issue preventing the more widespread use of these materials is that they undergo structural transformations (of up to ~10% lattice strains) during intercalation, which expand the material, nucleate microcracks, and, ultimately, lead to material failure. Besides the structural transformation of lattices, the crystallographic texture of the intercalation material plays a key role in governing ion-transport properties, generating phase separation microstructures, and elastically interacting with crystal defects. In this review, I provide an overview of how the structural transformation of lattices, phase transformation microstructures, and crystallographic defects affect the chemo-mechanical properties of intercalation materials. In each section, I identify the key challenges and opportunities to crystallographically design intercalation compounds to improve their properties and lifespans. I predominantly cite examples from the literature of intercalation cathodes used in rechargeable batteries, however, the identified challenges and opportunities are transferable to a broader range of intercalation compounds.