Substitutional carbon doping of the honeycomb-like boron nitride (BN) lattices in two-dimensional (nanosheets) and one-dimensional (nanoribbons and nanotubes) nanostructures was achieved via in situ electron beam irradiation in an energy-filtering 300 kV high-resolution transmission electron microscope using a C atoms feedstock intentionally introduced into the microscope. The C substitutions for B and N atoms in the honeycomb lattices were demonstrated through electron energy loss spectroscopy, spatially resolved energy-filtered elemental mapping, and in situ electrical measurements. The preferential doping was found to occur at the sites more vulnerable to electron beam irradiation. This transformed BN nanostructures from electrical insulators to conductors. It was shown that B and N atoms in a BN nanotube could be nearly completely replaced with C atoms via electron-beam-induced doping. The doping mechanism was proposed to rely on the knockout ejections of B and N atoms and subsequent healing of vacancies with supplying C atoms.