Understanding and utilizing structureperformance relationships in catalytic nanomaterials is the epitome of catalysis science. Knowledge at the atomic level can potentially allow rational design of more selective and energy efficient catalytic materials. Fischer-Tropsch synthesis on cobalt is an example of a complicated system that operates in a narrow process regime, and the nature of the reaction product is governed by numerous parameters. On an industrial model catalyst, we have simplified the structure of the active, metallic nanoparticles into predominantly hexagonal close packed structure via the use of a Co 2 C precursor. By varying the final reduction temperature, we could mildly modify catalyst microstructural properties at the nanoparticle (NP) level. Catalytic materials, although with minimal structural differences, showed significantly different performance. Evidently there is a narrow window for complete utilization of the hexagonal close packed Co crystallites that lays between removal of lattice carbon, that remains from the Co 2 C precursor, and the initiation of stacking disorder, due to transition to the face centered cubic Co structure. Fischer-Tropsch synthesis performance indicators show that Co NPs with minimum number of crystal defects outperform catalysts with lattice defects, either due to the existence of lattice carbon or stacking faults. Therefore, catalyst preparation and activation procedures probably should be designed targeting defect free Co crystallites.