A systematic study of the effect of different synthesis parameters on N incorporation into C nanotubes is presented. CNx nanotubes prepared by catalyzed pyrolysis of melamine exhibit a highly compartmentalized morphology with a remarkable periodicity structure along the nanotube axis. Spatially resolved electron energy loss spectroscopy (spectrum-imaging mode) indicates that the nanotubes are made of carbon and nitrogen, inhomogeneously distributed with an enrichment of carbon on the external surfaces. The evolution of the C-K-edge shape across the nanotube reveals a transition from a graphitic stacking on the outside to a disorganized-mixed type in the core of the nanotube. For the N-K edge, the situation is more complex. The fine structure of the N-K edge differs depending on the used catalyst, which indicates differences in the bonding configuration. When Ni is used as a catalyst, N replaces C in the graphitic structure whereas C-N pyridinic-like bonds are formed when the catalyst is Fe. The compartmentalized periodic morphology is the result of a systematic catalytic particle movement from the root of the nanotube to the tip. This displacement is defined by the nature of the catalytic particle, diffusion, and supersaturation (C/N) in the liquid particle and precipitation process.