We investigate the adsorption sites of 3d transition metal (TM) adatoms by means of low-temperature scanning tunneling microscopy and spectroscopy. Co and Ni adatoms were adsorbed on two types of graphene on SiC(0001), i.e., pristine epitaxial monolayer graphene (MLG) and quasi-free-standing monolayer graphene (QFMLG). In the case of QFMLG, two stable adsorption sites are identified, while in the case of MLG, only one adsorption site is observed. Our experimental results reveal the decoupling efficiency as a crucial parameter for determining the adsorption site as well as the electronic properties of 3d transition metal atoms on graphene. Furthermore, we show that Co atoms adsorbed on QFMLG are strong scattering potentials for Dirac fermions and cause intervalley scattering in their vicinity.