Abstract QTAIM atomic and bond properties as well as delocalization indices computed on B3LYP/6-311++(2d, 2p) and MP2/6-31++G(d, p) electron densities are employed to explain the protonation preference of indole for C3 site. In spite of displaying a very small increase of its total electron population, N1 is significantly stabilized in the preferred protonation due to an important loss of π electron population slightly exceeded by an increase of σ one. C2 and C8 are the atoms that reflect the largest changes of electron population in all C-protonations. 6-centre delocalization indices indicate that the preferred protonation increases the aromaticity of the benzenoid ring.