We report an electric field-driven chemical modification of bithiophene-based self-assembled monolayers (SAMs) in a large-area molecular junction. Upon in situ exposure to a high bias, the SAMs underwent an irreversible chemical modification, as confirmed by spectroscopic characterization, which we propose involves an oxidation process leading to dimerization of two bithiophene-based SAM molecules at the terminal thiophenes. This treatment resulted in a Pt/SAM//EGaIn molecular junction exhibiting an increased breakdown (short-circuit) voltage, while simultaneously achieving a higher rectification ratio compared with the device without SAM modification (R = 4.03 × 104 at an applied bias of ±3 V). This work demonstrates the potential of in situ tunable SAMs to significantly improve the performance and durability of molecular junctions, paving the way for more reliable and efficient molecular electronic devices.