The 2D crystal of sp2-bonded carbon atoms (graphene) is suitable for high-speed device applications owing to its excellent electronic properties and ultrathinness that suppresses the so-called short-channel effects. Unfortunately, however, graphene transistors have not exhibited high device performance as anticipated from their excellent electronic properties. One of the main causes is a high susceptibility of electronic properties to surrounding interfaces. Here, we show operando, i.e., bias-controlled, X-ray photoelectron nanospectroscopy on a transistor using epitaxial graphene on SiC as a channel. The operando photoelectron nanospectroscopy revealed that two types of unfavorable doping occur at the interfaces with electrodes, which can deteriorate the device performance of graphene transistors. Metals of source and drain electrodes are in direct contact with graphene. An equilibration between graphene and the metal produces a wide charge transfer region owing to a limited density of states near the Dirac point of graphene. The gate electric field permeates just outside the gate edge. The permeated electric field induces carrier doping into graphene just outside the gate edge. Thus, the operando photoelectron nanospectroscopy is proven useful in the science-based development of advanced devices.