It is known that graphene surface contaminations by residues affect drastically its intrinsic properties and cannot be avoided when chemical vapor deposited (CVD) graphene is transferred on other substrates. In this work, we investigate by X‐ray photoelectron spectroscopy and work function measurements using X‐ray photoemission electron microscopy the capabilities of high‐density plasmas to clean graphene. The evolution of different chemical species at surface is monitored as a function of plasma exposure. H2 plasmas are shown to clean efficiently PMMA residues from CVD graphene on Cu. However, when the same plasma is used on graphene transferred on SiO2/Si substrate a liftoff of the graphene layer is observed before the end of cleaning procedure. These results are discussed in terms of H+ penetration through graphene and H2 formation between the SiO2 substrate and graphene. Using Cl‐based chemistries, we found that the plasma is able to etch polymeric contamination at the graphene surface. It is also found that the plasma induces spreading of the Si nanoparticle contamination that hampers the cleaning process.