Graphene-enhanced Raman spectroscopy (GERS) is a technique to increase the Raman scattering of adsorbed probe molecules on graphene. Here we systematically explore the effect of the method used to transfer the CVD-grown graphene onto another substrate on Raman scattering. We have found that graphene transferred using poly methyl methacrylate (PMMA) produces 6 times the Raman scattering signal increase of that produced by graphene transferred using thermal release tape. The reason for this is that PMMA-assisted graphene contains a larger amount of defects such as carboxyl and hydroxyl groups that help the attachment of probe molecules to the graphene surface, leading to improved π-π∗ interactions and thus easier charge transfer between the probe molecules and graphene. Our results indicate the need for a much closer look at the functional groups of graphene which are different for the two transfer methods. © 2015 The Royal Society of Chemistry.