Organic/metal interfaces control the performance of many optoelectronic organic devices, including organic light-emitting diodes or field-effect transistors. Using scanning tunnelling microscopy, low-energy electron diffraction, X-ray photoemission spectroscopy, near-edge X-ray absorption fine structure spectroscopy and density functional theory calculations, we show that electron transfer at the interface between a metal surface and the organic electron acceptor tetracyano-p-quinodimethane leads to substantial structural rearrangements on both the organic and metallic sides of the interface. These structural modifications mediate new intermolecular interactions through the creation of stress fields that could not have been predicted on the basis of gas-phase neutral tetracyano-p-quinodimethane conformation.