Metal‐organic cages (MOCs) are popular host architectures assembled from ligands and metal ions/nodes. Assembling structurally complex, low‐symmetry MOCs with anisotropic cavities can be limited by the formation of statistical isomer libraries. We set out to investigate the use of primary coordination‐sphere engineering (CSE) to bias isomer selectivity within homo‐ and heteroleptic PdnL2n cages. Unexpected differences in selectivities between alternative donor groups led us to recognise the significant impact of the second coordination sphere on isomer stabilities. From this, molecular‐level insight into the origins of selectivity between cis and trans diastereoisomers was gained, highlighting the importance of both host‐guest and host‐solvent interactions, in addition to ligand design. This detailed understanding allows precision engineering of low‐symmetry MOC assemblies without wholesale redesign of the ligand framework, and fundamentally provides a theoretical scaffold for the development of stimuli‐responsive, shape‐shifting MOCs.