Herein we report the gas-sensitive properties to ammonia (at 2–10 ppm) of individual nanostructures of a polyaniline/nitrogen-doped carbon nanotube composite with a nitrogen content of 0 at.% (uCNTs), 2 at.% (N-CNTs) and 4 at.% (N+-CNTs). Doping of nanotubes with nitrogen was carried out in order to both reduce the electron work function, to form a potential barrier at the “PANI-CNTs” interface, and reduce the contribution of nanotubes to the composite conductivity. An increase in the nitrogen content in CNTs leads to an increase in conductivity, a decrease in the work function, and the formation of defects in the outer walls of CNTs. It was found that the structural and chemical state of the polymer layer of all composites is the same. However, polymer morphology on nanotubes changes dramatically with increasing nitrogen content in CNTs: a thin smooth layer on uCNTs, a globular layer on N-CNTs, and a thick layer with a sheet-like structure on N+-CNTs. All composites showed the same response time (~20 s) and recovery time (~120 s). Ammonia sensitivity was 10.5 ± 0.2, 15.3 ± 0.5 and 2.2 ± 0.1 ppm−1 for PANI/uCNTs, PANI/N-CNTs and PANI/N+-CNTs, respectively. Based on the results obtained here, we came to the conclusion that the morphological features of the polymer layer on CNTs with different nitrogen content have a dominant effect on the gas reaction than the change in the electronic properties of the polymer at the interface “PANI-CNT”.