Defects in atomically thin semiconductors and their moiré heterostructures have emerged as a unique testbed for quantum science. Strong light–matter coupling, large spin–orbit interaction and enhanced Coulomb correlations facilitate a spin–photon interface for future qubit operations and efficient single-photon quantum emitters. Yet, directly observing the relevant interplay of the electronic structure of a single defect with other microscopic elementary excitations on their intrinsic length, time and energy scales remained a long-held dream. Here we directly resolve in space, time and energy how a spin–orbit-split energy level of an isolated selenium vacancy in a moiré-distorted WSe2 monolayer evolves under the controlled excitation of lattice vibrations, using lightwave scanning tunnelling microscopy and spectroscopy. By locally launching a phonon oscillation and taking ultrafast energy-resolved snapshots of the vacancy’s states faster than the vibration period, we directly measure the impact of electron–phonon coupling in an isolated single-atom defect. The combination of atomic spatial, sub-picosecond temporal and millielectronvolt energy resolution marks a disruptive development towards a comprehensive understanding of complex quantum materials, where the key microscopic elementary interactions can now be disentangled, one by one.