<p>Two-dimensional atomic crystals (2DACs), which feature non-bonding van der Waals (vdW) gaps between crystalline atomic layers, allow selected atoms or molecules to intercalate. When confined within these vdW gaps, the intercalants can self-assemble into ordered interlayers between adjacent 2D atomic lattices, forming well-defined intercalated superlattices. These structures combine the intrinsic properties of solid-state 2DACs with the chemically programmable electronic, optical and magnetic functionalities of self-assembled atomic or molecular interlayers. As a result, they can integrate disparate quantum and collective phenomena, enabling device functionalities beyond the reach of conventional heterostructures. However, the synthesis of intercalated superlattices with specific functions is more complex than arbitrarily combining 2DACs with functional intercalants. Electronically, optically or magnetically active interlayers are inherently more reactive than passive species and are often incompatible with conventional chemical or electrochemical intercalation strategies. In this Review, we classify the functional building blocks used to construct functional intercalated superlattices and examine the key challenges and emerging strategies for their synthesis and assembly. Our goal is to establish guiding principles for the modular design and synthesis of chemically programmable intercalated superlattices with tailored electronic, optical, magnetic and quantum functionalities.</p>