Graphene is an excellent support film for high-resolution transmission electron microscopy (TEM) but its use with biological samples, notably in cryo-TEM, is hindered by its inherent hydrophobicity. Whereas surface treatments have been proposed to render graphene hydrophilic, they are often difficult to reproduce due to a lack of information on the structural changes that modify the wetting properties of graphene. This study aims to correlate the atomic structure of graphene with its wetting properties to allow a reproducible protocol to advance its application in cryo-TEM. We follow the change in the atomic structure of graphene as a function of low-energy hydrogen plasma treatment duration on monolayer graphene transferred onto TEM grids. With finely controlled plasma exposure, partial hydrogenation, monoatomic vacancies, and pores of a few nanometers are realized in the graphene. The introduction of defects (vacancies and pores) enables the formation of continuous layers of vitreous ice on TEM grids. Grids with defect-integrated graphene are reproduced and used in the vitrification of the mouse serotonin 5-HT3 receptor, a membrane protein. Single particle analysis of the membrane protein on graphene compared to conventional holey carbon film give insight into the strengths and discretions in using graphene membrane for protein structural studies.