The organization of nanostructures across extended length scales is a key challenge in the design of integrated materials with advanced functions. Current approaches tend to be based on physical methods, such as patterning, rather than the spontaneous chemical assembly and transformation of building blocks across multiple length scales. It should be possible to develop a chemistry of organized matter based on emergent processes in which time- and scale-dependent coupling of interactive components generate higher-order architectures with embedded structure. Herein we highlight how the interplay between aggregation and crystallization can give rise to mesoscale self-assembly and cooperative transformation and reorganization of hybrid inorganic–organic building blocks to produce single-crystal mosaics, nanoparticle arrays, and emergent nanostructures with complex form and hierarchy. We propose that similar mesoscale processes are also relevant to models of matrix-mediated nucleation in biomineralization.