We report on post-synthesis carbon doping of individual boron nitride nanotubes (BNNTs) via in situ electron-beam irradiation inside an energy-filtering 300 keV high-resolution transmission electron microscope. The substitution of C for B and N atoms in the honeycomb lattice was demonstrated through electron energy loss spectroscopy, spatially resolved energy-filtered elemental mapping, and in situ electrical measurements. Substitutional C doping transformed BNNTs from electrical insulators to conductors. In comparison with the existing post-synthesis doping methods for nanoscale materials (e.g., ion implantation and diffusion), the discovered electron-beam-induced doping is a well-controlled, little-damaging, room-temperature, and simple strategy that is expected to demonstrate great promise for post-synthesis doping of diverse nanomaterials in the future.