Controlled surface modification of boron nitride nanotubes has been achieved by gentle plasma treatment. Firstly, it was shown that an amorphous surface layer found on the outside of the nanotubes can be removed without damaging the nanotube structure. Secondly, it was shown that an oxygen plasma creates nitrogen vacancies that then allow oxygen atoms to be successfully substituted onto the surface of BNNTs. The percentage of oxygen atoms can be controlled by changing the input plasma energy and by the Ar plasma pre-treatment time. Finally, it has been demonstrated that nitrogen functional groups can be introduced onto the surface of BNNTs using an N(2) + H(2) plasma. The N(2) + H(2) plasma also created nitrogen vacancies, some of which led to surface functionalization while some underwent oxygen healing.