General routes to confined spaces of well-defined chemical composition and complex three-dimensional structure have long been sought by materials chemists. Here, we introduce metal-organic framework (MOF) materials as an ideal scaffold upon which such organized complexity can be built. Employing an orthogonal coordination strategy, we constructed a large-pore MOF material with two different modifiable linkers in well-defined positions relative to each other. The independent and quantitative covalent grafting of two distinct chemical groups onto these differently reactive linkers yielded a uniformly bifunctionalized MOF material. Not only does this methodology offer an efficient route via which the properties of well-defined microporous materials can be fine-tuned, but it also creates a solid-state platform for synthetically accessing constructs that better emulate the well-ordered intricacy of biological structures.