Metal-organic cages (MOCs) have become an intensely studied class of abiotic host molecules. This is due to the ability to generate a myriad of polyhedral architectures from relatively simple, and minimal numbers of, components in high yield and under thermodynamic control. The encapsulation of molecular guests within the nanoscale, confined cavities of these cages frequently draws comparisons with enzymatic binding sites. In this regard, the ostensible ease with which chemical modifications can be made to these internal cavities adds to their attractiveness, as they can be readily tailored with a high degree of precision. In this Feature Article, the ways in which the cavities of MOCs can be engineered at the molecular level will be looked at. The discussion will be divided across three key parameters: size, shape and functionality. Most concepts will be exemplified with a focus on the Pd2L4 class of assemblies due to their relative structural simplicity and the wealth of studies reported in the literature. The core principles discussed will, however, be generalisable to other classes of MOCs, and abiotic host systems as a whole. Gaining increasing mastery over the fine tuning of MOC cavity properties, whilst retaining facile, high-fidelity self-assembly processes, will lead to ever more precise engineering of the cavities of artificial host systems with complex and highly specific functionality.