We describe the self-assembly of gold and iron oxide nanoparticles regulated by a chemical reaction cycle that hydrolyzes a carbodiimide-based fuel. In a reaction with the chemical fuel, the nanoparticles are chemically activated to a state that favors assembling into clusters. The activated state is metastable and decays to the original precursor reversing the assembly. The dynamic interplay of activation and deactivation results in a material of which the behavior is regulated by the amount of fuel added to the system; they either did not assemble, assembled transiently, or assembled permanently in kinetically trapped clusters. Because of the irreversibility of the kinetically trapped clusters, we found that the behavior of the self-assembly was prone to hysteresis effects. The final state of the system in the energy landscape depended on the pathway of preparation. For example, when a large amount of fuel was added at once, the material would end up kinetically trapped in a local minimum. When the same amount of fuel was added in small batches with sufficient time for the system to re-equilibrate, the final state would be the global minimum. A better understanding of pathway complexity in the energy landscape is crucial for the development of fuel-driven supramolecular materials.