Controlling the electrical conductance and in particular the occurrence of quantum interference in single-molecule junctions through gating effects has potential for the realization of high-performance functional molecular devices. In this work we used an electrochemically gated, mechanically controllable break junction technique to tune the electronic behaviour of thiophene-based molecular junctions that show destructive quantum interference features. By varying the voltage applied to the electrochemical gate at room temperature, we reached a conductance minimum that provides direct evidence of charge transport controlled by an anti-resonance arising from destructive quantum interference. Our molecular system enables conductance tuning close to two orders of magnitude within the non-faradaic potential region, which is significantly higher than that achieved with molecules not showing destructive quantum interference. Our experimental results, interpreted using quantum transport theory, demonstrate that electrochemical gating is a promising strategy for obtaining improved in situ control over the electrical performance of interference-based molecular devices. © 2019, The Author(s), under exclusive licence to Springer Nature Limited.