We report on electric-field-induced irreversible structural modifications in pentacene thin films after long-term operation of organic field-effect transistor (OFET) devices. Micro-Raman spectroscopy allows for the analysis of the microstructural modifications of pentacene in the small active channel of OFET during device operation. The results suggest that the herringbone packing of pentacene molecules in a solid film is affected by an external electric field, particularly the source-to-drain field that parallels the a–b lattice plane. The analysis of vibrational frequency and Davydov splitting in the Raman spectra reveals a singular behavior suggesting a reduced separation distance between pentacene molecules after long-term operations and, thus, large intermolecular interactions. These results provide evidence for improved OFET performance after long-term operation, related to the microstructures of organic semiconductors. It is known that the application of large electric fields alters the semiconductor properties of the material owing to the generation of defects and the trapping of charges. However, we first suggest that large electric fields may alter the molecular geometry and further induce structural phase transitions in the pentacene films. These results provide a basis for understanding the improved electronic properties in test devices after long-term operations, including enhanced field-effect mobility, improved on/off current ratio, sharp sub-threshold swing, and a slower decay rate in the output drain current. In addition, the effects of source-to-drain electric field, gate electric field, current and charge carriers, and thermal annealing on the pentacene films during OFET operations are discussed.