The sintering of iron nanoparticles on carbon nanotubes (CNTs) under different atmospheres was investigated. CNTs were first treated with HNO3 vapor at 200 °C to obtain O-functionalized CNTs (OCNTs). The OCNTs were treated in ammonia at 400 °C to obtain N-doped CNTs (NCNTs). Highly dispersed FeOx nanoparticles were subsequently deposited by chemical vapor deposition from ferrocene under oxidizing conditions. The obtained FeOx/OCNT and FeOx/NCNT samples were allowed to sinter at 500 °C under flowing helium, hydrogen, or ammonia. The samples were studied by X-ray diffraction, transmission electron microscopy, and X-ray photoelectron spectroscopy. A significant increase in particle size and a decrease in Fe surface atomic concentration were observed in all the sintered samples. The sintering on OCNTs was more severe than on NCNTs, which can be attributed to stronger metal-substrate interactions and a higher amount of surface defects on NCNTs. The applied gas atmosphere had a substantial influence on the sintering behavior of the nanoparticles: treatment in helium led to the growth of particles and a significant widening of particle size distributions, whereas treatment in hydrogen or ammonia resulted in the growth of particles, but not in the widening of particle size distributions.