Complex structures from nanoparticles are found in rocks, soils, and sea sediments but the mechanisms of their formation are poorly understood, which causes controversial conclusions about their genesis. Here we show that graphene quantum dots (GQDs) can assemble into complex structures driven by coordination interactions with metal ions commonly present in environment and serve a special role in Earth's history, such as Fe3+ and Al3+. GQDs self‐assemble into mesoscale chains, sheets, supraparticles, nanoshells, and nanostars. Specific assembly patterns are determined by the effective symmetry of the GQDs when forming the coordination assemblies with the metal ions. As such, maximization of the electronic delocalization of π‐orbitals of GQDs with Fe3+ leads to GQD‐Fe‐GQD units with D2 symmetry, dipolar bonding potential, and linear assemblies. Taking advantage of high electron microscopy contrast of carbonaceous nanostructures in respect to ceramic background, the mineralogical counterparts of GQD assemblies are found in mineraloid shungite. These findings provide insight into nanoparticle dynamics during the rock formation that can lead to mineralized structures of unexpectedly high complexity.