Brain-computer interfaces (BCIs) can be used to induce neural plasticity in the human nervous system by pairing motor cortical activity with relevant afferent feedback, which can be used in neurorehabilitation. The aim of this study was to identify the optimal type or combination of afferent feedback modalities to increase cortical excitability in a BCI training intervention. In three experimental sessions, 12 healthy participants imagined a dorsiflexion that was decoded by a BCI which activated relevant afferent feedback: (1) electrical nerve stimulation (ES) (peroneal nerve—innervating tibialis anterior), (2) passive movement (PM) of the ankle joint, or (3) combined electrical stimulation and passive movement (Comb). The cortical excitability was assessed with transcranial magnetic stimulation determining motor evoked potentials (MEPs) in tibialis anterior before, immediately after and 30 min after the BCI training. Linear mixed regression models were used to assess the changes in MEPs. The three interventions led to a significant (p < 0.05) increase in MEP amplitudes immediately and 30 min after the training. The effect sizes of Comb paradigm were larger than ES and PM, although, these differences were not statistically significant (p > 0.05). These results indicate that the timing of movement imagery and afferent feedback is the main determinant of induced cortical plasticity whereas the specific type of feedback has a moderate impact. These findings can be important for the translation of such a BCI protocol to the clinical practice where by combining the BCI with the already available equipment cortical plasticity can be effectively induced. The findings in the current study need to be validated in stroke populations.