We showed that a chain of nanomagnetic tunnel junctions (MTJs) devices can be electrically addressed individually, in situ, in a transmission electron microscope, such that transport properties can be in principle, quantitatively correlated with each device’s defects and microstructure. A unique energy barrier was obtained for each device measured. Additionally, in situ tunneling magnetoresistance (TMR) measurements were obtained for a subset of devices. We found that TMR values for our nano-MTJs were generally smaller than TMR in the unpatterned film.