Motion has an adverse effect on spectral quality and needs to be properly identified in MR spectroscopy (MRS) scans. Spectral subtraction-based techniques like J-difference editing are prone to be affected more by subject motion where motion can result in false peaks or inefficient subtraction of peaks. Introducing a water signal-based interleaved navigator scan in the MEGA point-resolved spectroscopy (MEGA-PRESS) sequence and acquiring data on a shot-by-shot basis, subject motion inside a scanner was tracked and motion-corrupted data were identified and excluded from the dataset. Performing a gamma-aminobutyric acid (GABA) editing scan at the occipital cortex, it was possible to retrieve a properly edited GABA spectrum from a dataset otherwise to be discarded due to motion. This study demonstrates the importance of independent motion assessment in J-difference editing.