Nitrogen-doped carbon nanomaterials show unique properties in catalysis both as an active component and as a support. The oxidized and N-doped graphene nanoflakes (GNFs) of low domain size (10-30 nm) have been studied in present work as supports for cobalt-based Fischer-Tropsch catalysts. Three supports with different types of dominating nitrogen species were synthesized and the effect of both the nature and localization of nitrogen species in the support on the structure and performance of 10 wt.% Co catalysts was investigated. Varying the synthesis technique and post-synthesis treatment, the cobalt particle size and hence the activity of catalyst can be tuned. The catalysts supported on oxidized pristine and N-doped GNFs were found to be the most active. Transformations of N-groups during catalyst preparation and reduction were observed. In the case of edge localization of N-groups the cross-linking of support particles was detected that led to the diffusion hindering and low CO conversion over corresponding catalyst.