Molecules intercalate at the graphene/metal interface even though defect-free graphene is impermeable to any atomic and molecular species in the gas and liquid phase, except hydrogen. The mechanism of molecular intercalation is still a big open question. In this Letter, by means of a combined experimental (STM, XPS, and LEED) and theoretical (DFT) study, we present a proof of how CO molecules succeed in permeating the graphene layer and get into the confined zone between graphene and the Ni(111) surface. The presence of N-dopants in the graphene layer is found to highly facilitate the permeation process, reducing the CO threshold pressure by more than one order of magnitude, through the stabilization of multiatomic vacancy defects that are the open doors to the bidimensional nanospace, with crucial implications for the catalysis under cover and for the graphene-based electrochemistry.