We probe the local inhomogeneities of the electronicproperties of graphene at the nanoscale usingscanning probe microscopy techniques. First, wefocus on the study of the electronic inhomogeneitiescaused by the graphene-substrate interaction ingraphene samples exfoliated on silicon oxide. Wefind that charged impurities, present in the graphenesubstrateinterface, perturb the carrier densitysignificantly and alter the electronic properties ofgraphene. This finding helps to understand theobserved device-to-device variation typically observedin graphene-based electronic devices. Second, weprobe the effect of chemical modification in theelectronic properties of graphene, grown by chemicalvapour deposition on nickel. We find that both thechemisorption of hydrogen and the physisorption ofporphyrin molecules strongly depress theconductance at low bias indicating the opening of abandgap in graphene, paving the way towards thechemical engineering of the electronic properties ofgraphene.