Colloidal hybrid nanoparticles contain multiple nanoscale domains fused together by solid-state interfaces. They represent an emerging class of multifunctional lab-on-a-particle architectures that underpin future advances in solar energy conversion, fuel-cell catalysis, medical imaging and therapy, and electronics. The complexity of these ‘artificial molecules’ is limited ultimately by the lack of a mechanism-driven design framework. Here, we show that known chemical reactions can be applied in a predictable and stepwise manner to build complex hybrid nanoparticle architectures that include M–Pt–Fe3O4 (M = Au, Ag, Ni, Pd) heterotrimers, MxS–Au–Pt–Fe3O4 (M = Pb, Cu) heterotetramers and higher-order oligomers based on the heterotrimeric Au–Pt–Fe3O4 building block. This synthetic framework conceptually mimics the total-synthesis approach used by chemists to construct complex organic molecules. The reaction toolkit applies solid-state nanoparticle analogues of chemoselective reactions, regiospecificity, coupling reactions and molecular substituent effects to the construction of exceptionally complex hybrid nanoparticle oligomers.