This chapter summarizes how brain imaging can be used in combination with non-invasive transcranial stimulation to probe and induce neuroplasticity in the human brain. We aim to give a conceptual account and highlight exemplary studies. We showcase the scientific and clinical potentials of studies focusing on the combination of transcranial magnetic stimulation (TMS) with Magnetic Resonance Imaging (MRI) or Magnetic Resonance Spectroscopy (MRS). MRI and MRS can be used before brain stimulation to identify target networks and loci but also to inform individual dosing. After a brain stimulation session, MRI and MRS can be used to pinpoint how the stimulation protocol alters brain function, structure, or metabolism and relate these after-effects to behavioral and clinical outcomes. Complementing these “offline” approaches, TMS can also be applied “online” during MRI or MRS to delineate how stimulation acutely engages the stimulated brain regions and networks. In this case, it is critical to account for confounds introduced by off-target stimulation of peripheral structures of the nervous system that may not only confound MR-based readouts but also induce neuroplastic phenomena.