The present study aims to gain insights into the effects of training with a motor imagery (MI)-based brain-computer interface (BCI) on activation patterns of the sensorimotor cortex. We used functional near-infrared spectroscopy (fNIRS) and electroencephalography (EEG) to investigate long-term training effects across 10 sessions using a 2-class (right hand and feet) MI-based BCI in fifteen subjects. In the course of the training a significant enhancement of activation pattern emerges, represented by an [oxy-Hb] increase in fNIRS and a stronger event-related desynchronization in the upper β-frequency band in the EEG. These effects were only visible in participants with relatively low BCI performance (mean accuracy ≤ 70%). We found that training with an MI-based BCI affects cortical activation patterns especially in users with low BCI performance. Our results may serve as a valuable contribution to the field of BCI research and provide information about the effects that training with an MI-based BCI has on cortical activation patterns. This might be useful for clinical applications of BCI which aim at promoting and guiding neuroplasticity.