When the separation of two surfaces approaches sub-nanometre scale, the boundary between the two most fundamental heat transfer modes, heat conduction by phonons and radiation by photons, is blurred. Here we develop an atomistic framework based on microscopic Maxwell's equations and lattice dynamics to describe the convergence of these heat transfer modes and the transition from one to the other. For gaps >1 nm, the predicted conductance values are in excellent agreement with the continuum theory of fluctuating electrodynamics. However, for sub-nanometre gaps we find the conductance is enhanced up to four times compared with the continuum approach, while avoiding its prediction of divergent conductance at contact. Furthermore, low-frequency acoustic phonons tunnel through the vacuum gap by coupling to evanescent electric fields, providing additional channels for energy transfer and leading to the observed enhancement. When the two surfaces are in or near contact, acoustic phonons become dominant heat carriers.