The coherent interaction between quantum emitters and photonic modes in cavities underlies many of the current strategies aiming at generating and controlling photonic quantum states. A plasmonic nanocavity provides a powerful solution for reducing the effective mode volumes down to nanometre scale, but spatial control at the atomic scale of the coupling with a single molecular emitter is challenging. Here we demonstrate sub-nanometre spatial control over the coherent coupling between a single molecule and a plasmonic nanocavity in close proximity by monitoring the evolution of Fano lineshapes and photonic Lamb shifts in tunnelling electron-induced luminescence spectra. The evolution of the Fano dips allows the determination of the effective interaction distance of ∼1 nm, coupling strengths reaching ∼15 meV and a giant self-interaction induced photonic Lamb shift of up to ∼3 meV. These results open new pathways to control quantum interference and field-matter interaction at the nanoscale.