The energy-level alignment of molecular transistors can be controlled by external gating to move molecular orbitals with respect to the Fermi levels of the source and drain electrodes. Two-terminal molecular tunnelling junctions, however, lack a gate electrode and suffer from Fermi-level pinning, making it difficult to control the energy-level alignment of the system. Here we report an enhancement of 2 orders of magnitude of the tunnelling current in a two-terminal junction via chemical molecular orbital control, changing chemically the molecular component between a stable radical and its non-radical form without altering the supramolecular structure of the junction. Our findings demonstrate that the energy-level alignment in self-assembled monolayer-based junctions can be regulated by purely chemical modifications, which seems an attractive alternative to control the electrical properties of two-terminal junctions.