||Free-standing graphene membranes are a promising candidate for use as in-situ environmental windows in X-ray (electron) microscopy. In this study, graphene membranes were used as the working electrode, and cobalt nanoparticles (Co-NPs) were grown directly on top of the graphene through electrochemical deposition for interfacial variation. The electronic structure and the chemical bonding states of the Co-NPs and the graphene materials were examined by using the high spatial resolution and element-specific properties of scanning transmission X-ray microscopy. X-ray absorption spectra of C, O, and Co revealed that the Co-NP size increased in accordance with the oxidation state (Co0/2+/3+), depending on the configuration of carbon bonding (C–C/C–OH/HO–C=O/O–C(O)–O/C=O–like state). We conducted a spectral comparison of the dipped graphene and the electrodeposited Co–graphene sample, which revealed an increase in C–OH formation before Co-NPs growth. In addition to electron transfer and electrochemical reduction, the oxidation evolution from C–OH to HO–C=O (or a defect) and the O–C(O)–O (or C=O) state paralleled the increase in Co-NPs size. We curve-fitted the results to demonstrate the reduction in chemical structure from mixing Co2+/3+ to Co3+/2+/0, and to explain the interfacial modulation and the unique metal Co0 layer on the surface of the Co-NPs. Our results provide information for the design of a reliable graphene window and offer an example for the interpretation of experimental X-ray (electron) microscopy.